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The current mutation

ID: V6638
DNA: 5619C>T
Protein: Y1873Y
Position: 5884








COV2Var annotation categories







Summary information of mutation (5619C>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   5884
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   synonymous_variant
  DNA Level   DNA Mutation: 5619C>T
  Ref Seq: C
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: Y1873Y
  Protein 3-letter Mutation: Tyr1873Tyr

Overview of the genomic positions of Mutation.
Note: The annotated 12 genes were retrieved from GeneBank (Accession: NC_045512.2). "MP" represents genomic position of mutation.





Analyzing the distribution of mutation (5619C>T) across geographic regions, temporal trends, and lineages

The count of genome sequences harboring this mutation and its distribution across global regions offer insights into regional variations.
Note: The distribution of mutation across 218 geographical regions. Color representation of genome sequence counts. The data is obtained from GISAID's metadata, specifically capturing the regional distribution of genomic sequences.



The dynamic count of genome sequences containing this mutation over time.
Note: Clicking the "Count" or "Cumulative Count" button toggles the view. Count represents the number of genome sequences per month. Cumulative count represents the accumulated total count up to the respective month. The data is obtained from GISAID's metadata, specifically capturing the collection date of genomic sequences.



For every time point represented in the graph above, identifying the top 3 lineages with the highest count of genome sequences carrying this mutation aids in pinpointing noteworthy lineages for further analysis.
Note: Users can filter the lineages by entering a "Year-Month" term in the search box. For example, entering 2020-01 will display lineages that appeared in January 2020. The data is obtained from GISAID's metadata, specifically capturing the collection date of genomic sequences.

Collection date Lineage Total lineage monthly counts Lineage-specific monthly counts Lineage-specific monthly frequency
2020-10 B.1.1.196 302 124 4.11e-1
2020-10 B.1.1.216 302 67 2.22e-1
2020-10 B.1.1.389 302 24 7.95e-2
2020-11 B.1.1.216 668 95 1.42e-1
2020-11 B.1.1.196 668 94 1.41e-1
2020-11 AM.4 668 80 1.20e-1
2020-12 B.1.1.216 871 287 3.30e-1
2020-12 B.1.474 871 117 1.34e-1
2020-12 B.1.1.389 871 80 9.18e-2
2020-02 B.1 1 1 1.00e+0
2020-03 B.1 52 34 6.54e-1
2020-03 B.31 52 5 9.62e-2
2020-03 B.1.1 52 4 7.69e-2
2020-04 B.1 41 24 5.85e-1
2020-04 B.1.1 41 7 1.71e-1
2020-04 B.1.119 41 4 9.76e-2
2020-05 B.1 77 38 4.94e-1
2020-05 B.1.1.216 77 26 3.38e-1
2020-05 B.1.1 77 7 9.09e-2
2020-06 B.1.1 36 9 2.50e-1
2020-06 B.1.1.389 36 8 2.22e-1
2020-06 B.1.1.216 36 7 1.94e-1
2020-07 B.1 82 23 2.80e-1
2020-07 B.1.1.174 82 16 1.95e-1
2020-07 B.1.1.389 82 14 1.71e-1
2020-08 B.1.1.174 127 28 2.20e-1
2020-08 B.1.1.216 127 21 1.65e-1
2020-08 B.1.425 127 18 1.42e-1
2020-09 B.1.1.196 243 80 3.29e-1
2020-09 B.1.1.216 243 59 2.43e-1
2020-09 B.1.1.389 243 26 1.07e-1
2021-01 B.1.1.214 1054 275 2.61e-1
2021-01 B.1.1.216 1054 134 1.27e-1
2021-01 B.1.474 1054 95 9.01e-2
2021-10 AY.3 1173 389 3.32e-1
2021-10 AY.4 1173 137 1.17e-1
2021-10 AY.43 1173 64 5.46e-2
2021-11 AY.3 2063 466 2.26e-1
2021-11 AY.43 2063 225 1.09e-1
2021-11 AY.103 2063 223 1.08e-1
2021-12 AY.3 2061 318 1.54e-1
2021-12 AY.103 2061 271 1.31e-1
2021-12 AY.43 2061 206 1.00e-1
2021-02 B.1.474 828 153 1.85e-1
2021-02 B.1.1.216 828 135 1.63e-1
2021-02 B.1.1.7 828 103 1.24e-1
2021-03 B.1.1.7 861 390 4.53e-1
2021-03 B.1.1.216 861 85 9.87e-2
2021-03 B.1.474 861 33 3.83e-2
2021-04 B.1.1.7 750 449 5.99e-1
2021-04 P.1 750 87 1.16e-1
2021-04 B.1.637 750 24 3.20e-2
2021-05 B.1.1.7 529 357 6.75e-1
2021-05 P.1 529 64 1.21e-1
2021-05 B.1.438.1 529 16 3.02e-2
2021-06 B.1.1.7 440 235 5.34e-1
2021-06 P.1 440 107 2.43e-1
2021-06 B.1.617.2 440 20 4.55e-2
2021-07 B.1.1.7 558 134 2.40e-1
2021-07 P.1 558 75 1.34e-1
2021-07 AY.122 558 52 9.32e-2
2021-08 AY.29 976 213 2.18e-1
2021-08 AY.3 976 206 2.11e-1
2021-08 AY.37 976 123 1.26e-1
2021-09 AY.3 956 308 3.22e-1
2021-09 AY.4 956 76 7.95e-2
2021-09 AY.37 956 63 6.59e-2
2022-01 BA.1.1 1068 174 1.63e-1
2022-01 AY.29 1068 164 1.54e-1
2022-01 BA.1.17 1068 120 1.12e-1
2022-10 BA.5.1.10 606 149 2.46e-1
2022-10 BQ.1 606 70 1.16e-1
2022-10 BA.5.2.34 606 53 8.75e-2
2022-11 BQ.1 646 139 2.15e-1
2022-11 BF.5 646 88 1.36e-1
2022-11 BA.5.2.34 646 81 1.25e-1
2022-12 BQ.1 625 79 1.26e-1
2022-12 BF.5 625 69 1.10e-1
2022-12 BQ.1.1 625 57 9.12e-2
2022-02 BA.2 1018 373 3.66e-1
2022-02 BA.1.1 1018 270 2.65e-1
2022-02 BA.1 1018 69 6.78e-2
2022-03 BA.2 1287 963 7.48e-1
2022-03 BA.1.1 1287 87 6.76e-2
2022-03 BA.2.9 1287 66 5.13e-2
2022-04 BA.2 914 687 7.52e-1
2022-04 BA.2.9 914 86 9.41e-2
2022-04 BA.2.10 914 38 4.16e-2
2022-05 BA.2 713 415 5.82e-1
2022-05 BA.2.36 713 109 1.53e-1
2022-05 BA.2.9 713 69 9.68e-2
2022-06 BA.2 639 137 2.14e-1
2022-06 BA.5.1.10 639 122 1.91e-1
2022-06 BA.5.5 639 64 1.00e-1
2022-07 BA.5.1.10 647 216 3.34e-1
2022-07 BA.5.5 647 103 1.59e-1
2022-07 BE.1 647 93 1.44e-1
2022-08 BA.5.1.10 453 181 4.00e-1
2022-08 BA.5.5 453 46 1.02e-1
2022-08 BA.5 453 38 8.39e-2
2022-09 BA.5.1.10 474 160 3.38e-1
2022-09 BA.5.1.4 474 39 8.23e-2
2022-09 BA.5 474 37 7.81e-2
2023-01 XBB.1.5 402 49 1.22e-1
2023-01 BN.1.3 402 46 1.14e-1
2023-01 BQ.1.1 402 44 1.09e-1
2023-02 BQ.1.1 102 17 1.67e-1
2023-02 BN.1.3 102 16 1.57e-1
2023-02 XBB.1.5 102 12 1.18e-1

The count of genome sequences and the frequency of this mutation in each lineage.
Note: Displaying mutation frequencies (>0.01) among 2,735 lineages. Mutation Count represents the count of sequences carrying this mutation. Users can filter the lineages by entering a search term in the search box. For example, entering "A.1" will display A.1 lineages. The data is obtained from GISAID's metadata, specifically capturing the lineage of genomic sequences. Mutation count: Count of sequences carrying this mutation.

Mutation ID Lineage Mutation frequency Mutation count Earliest lineage emergence Latest lineage emergence
V6638 B.1.1.214 2.10e-2 399 2020-2-22 2021-7-29
V6638 BA.2.36 1.64e-2 182 2021-11-15 2023-1-20
V6638 BA.5.1.10 7.42e-2 898 2022-2-26 2023-1-30
V6638 AY.1 1.19e-2 40 2021-3-31 2022-3-14
V6638 AY.37 8.75e-2 296 2021-2-18 2022-1-6
V6638 AY.4.9 2.77e-2 68 2020-8-11 2022-6-7
V6638 AY.91 1.68e-2 27 2021-2-8 2022-5-22
V6638 B.1.1.216 9.54e-1 946 2020-5-6 2022-7-9
V6638 B.1.177.46 7.37e-2 80 2020-10-29 2021-5-27
V6638 B.1.177.75 2.62e-2 24 2020-9-2 2021-10-8
V6638 B.1.389 1.11e-2 10 2020-8-2 2021-3-15
V6638 BA.5.1.26 1.67e-2 13 2022-6-8 2023-2-16
V6638 BA.5.1.4 5.81e-2 76 2022-5-25 2022-12-14
V6638 BE.1.1.1 2.02e-2 57 2022-2-6 2023-2-14
V6638 XBB 1.18e-2 30 2022-1-10 2023-2-21
V6638 BA.5.2.34 4.16e-2 190 2022-1-2 2023-2-19
V6638 BQ.1 1.20e-2 324 2021-12-28 2023-2-22
V6638 A.2.5.3 4.26e-2 4 2021-2-23 2021-9-21
V6638 AM.1 7.50e-1 6 2020-11-9 2021-2-9
V6638 AM.2 8.00e-1 12 2020-8-3 2021-2-21
V6638 AM.3 8.33e-1 25 2020-10-30 2020-12-8
V6638 AM.4 7.89e-1 157 2020-11-5 2021-5-2
V6638 AY.4.2.4 1.79e-1 31 2021-5-21 2022-1-25
V6638 B.1.1.174 1.26e-1 40 2020-3-15 2021-8-21
V6638 B.1.1.196 9.51e-1 155 2020-8-26 2020-12-30
V6638 B.1.119 2.13e-2 2 2020-3-12 2021-1-28
V6638 B.1.1.368 1.96e-2 6 2020-6-9 2021-9-14
V6638 B.1.1.389 9.70e-1 159 2020-6-18 2021-4-7
V6638 B.1.1.413 1.69e-2 3 2020-9-7 2021-7-29
V6638 B.1.1.58 1.37e-2 2 2020-4-8 2021-7-16
V6638 B.1.177.53 1.17e-2 4 2020-8-3 2021-7-20
V6638 B.1.201 1.18e-2 2 2020-3-6 2020-12-28
V6638 B.1.237 7.03e-2 13 2020-4-24 2021-8-4
V6638 B.1.306 1.09e-2 2 2020-6-3 2021-3-8
V6638 B.1.348 8.46e-1 44 2020-10-7 2021-1-15
V6638 B.1.36.20 3.39e-2 2 2020-8-20 2021-4-25
V6638 B.1.401 3.30e-2 6 2020-6-4 2021-3-8
V6638 B.1.425 6.56e-2 21 2020-5-7 2022-4-20
V6638 B.1.474 9.47e-1 464 2020-9-21 2021-5-19
V6638 B.1.478 2.38e-2 3 2020-5-15 2021-3-5
V6638 B.1.510 2.50e-1 6 2020-3-6 2021-1-5
V6638 B.1.573 3.66e-2 6 2020-6-24 2020-10-3
V6638 B.1.603 8.05e-2 7 2020-11-10 2021-4-17
V6638 B.1.616 9.46e-1 35 2021-1-29 2021-4-23
V6638 B.31 2.06e-2 5 2020-3-3 2020-7-3
V6638 BA.2.69 1.37e-2 3 2022-1-5 2022-7-14
V6638 BN.1.3.2 1.04e-2 4 2022-11-7 2023-2-18
V6638 BN.6 3.87e-2 13 2022-6-25 2023-2-13
V6638 BQ.1.20 2.84e-2 6 2022-8-29 2023-2-13
V6638 BQ.1.27 3.49e-2 9 2022-10-7 2023-2-11
V6638 C.18 1.60e-2 3 2020-7-1 2021-10-8
V6638 CH.1.1.4 1.09e-2 3 2022-7-28 2023-2-20
V6638 P.1.8 3.39e-2 10 2021-5-3 2021-10-25
V6638 P.4 1.48e-2 4 2021-2-17 2021-9-9
V6638 P.7 2.70e-2 7 2020-7-1 2021-5-30
V6638 Q.8 1.27e-2 4 2021-3-7 2021-10-30
V6638 XBC.1.2.1 1.95e-1 36 2022-11-9 2023-2-17
V6638 AY.3 1.12e-2 1752 2020-8-1 2022-5-26






Examining mutation (5619C>T) found in abundant sequences of non-human animal hosts

Exploring mutation presence across 35 non-human animal hosts for cross-species transmission.
Note: We retained the mutation that appear in at least three non-human animal hosts' sequences. The data is obtained from GISAID's metadata, specifically capturing the host of genomic sequences.

Animal host Lineage Source region Collection date Accession ID
Rhinolophus pusillus A Laos 2020-7-7 EPI_ISL_4302645
Odocoileus virginianus B.1.2 USA 2020-12-10 EPI_ISL_5804776
Neogale vison B.1 Lithuania 2021-11-26 EPI_ISL_10497475
Rhinolophus marshalli BA.1 Laos 2020-7-10 EPI_ISL_4302647
Rhinolophus malayanus BA.1 Laos 2020-7-5 EPI_ISL_4302644
Odocoileus virginianus AY.3 USA 2022-3-10 EPI_ISL_16467176




Association between mutation (5619C>T) and patients of different ages, genders, and statuses

Note: The logistic regression model was employed to examine changes in patient data before and after the mutation. The logistic regression model was conducted using the glm function in R. The data is obtained from GISAID's metadata, specifically capturing the patient status, gender, and age of genomic sequences.

Analyzing the association between mutation and patient status.
Note: we categorized the data into different patient statuses (ambulatory, deceased, homebound, hospitalized, mild, and recovered) based on GISAID classifications. In the analysis exploring the association between mutation and patient status, the model included mutation, patient status, patient age, gender, sequence region of origin, and sequence collection time point. In the 'increase' direction of the mutation, it means that when this mutation occurs, it increases the corresponding effect proportion. In the 'decrease' direction of the mutation, it means that when this mutation occurs, it decreases the corresponding effect proportion. A p-value lower than 0.001 signifies a notable differentiation between the population with and without the mutation.

Attribute Effect Estimate SE Z-value P-value Direction
Patient status Ambulatory -4.15e-1 6.63e-1 -6.26e-1 5.31e-1 Decrease
Deceased 7.48e-1 3.77e-1 1.98e+0 4.75e-2 Increase
Homebound 2.93e+0 8.64e-1 3.40e+0 6.85e-4 Increase
Hospitalized 5.12e-1 2.44e-1 2.10e+0 3.61e-2 Increase
Mild 5.62e-1 4.29e-1 1.31e+0 1.91e-1 Increase
Recovered -1.55e+0 3.03e-1 -5.12e+0 3.07e-7 Decrease

Analyzing the association between mutation and patient status.
Note: we categorized the data into different patient age (0-17, 18-39, 40-64, 65-84, and 85+). In the analysis exploring the association between mutation and patient age, the model included mutation, patient age, gender, sequence region of origin, and sequence collection time point. In the 'increase' direction of the mutation, it means that when this mutation occurs, it increases the corresponding effect proportion. In the 'decrease' direction of the mutation, it means that when this mutation occurs, it decreases the corresponding effect proportion. A p-value lower than 0.001 signifies a notable differentiation between the population with and without the mutation.

Attribute Effect Estimate SE Z-value P-value Direction
Patient age, years 0-17 -1.78e-1 6.62e-2 -2.69e+0 7.14e-3 Decrease
18-39 -3.56e-2 3.68e-2 -9.65e-1 3.34e-1 Decrease
40-64 6.06e-2 3.71e-2 1.63e+0 1.03e-1 Increase
65-84 1.22e-1 5.09e-2 2.40e+0 1.63e-2 Increase
>=85 -2.36e-2 9.88e-2 -2.39e-1 8.11e-1 Decrease

Analyzing the association between mutation and patient status.
Note: we categorized the data into different patient gender (male and female). In the analysis exploring the association between mutation and patient gender, the model included mutation, patient gender, patient age, sequence region of origin, and sequence collection time point. In the 'increase' direction of the mutation, it means that when this mutation occurs, it increases the corresponding effect proportion. In the 'decrease' direction of the mutation, it means that when this mutation occurs, it decreases the corresponding effect proportion. A p-value lower than 0.001 signifies a notable differentiation between the population with and without the mutation.

Attribute Effect Estimate SE Z-value P-value Direction
Patient gender Male 8.03e-2 3.57e-2 2.25e+0 2.44e-2 Increase





Investigating natural selection at mutation (5619C>T) site for genetic adaptation and diversity

Note: Investigating the occurrence of positive selection or negative selection at this mutation site reveals implications for genetic adaptation and diversity.

The MEME method within the HyPhy software was employed to analyze positive selection. MEME: episodic selection.
Note: List of sites found to be under episodic selection by MEME (p < 0.05). "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site P-value Lineage Method

The FEL method within the HyPhy software was employed to analyze both positive and negative selection. FEL: pervasive selection on samll datasets.
Note: List of sites found to be under pervasive selection by FEL (p < 0.05). A beta value greater than alpha signifies positive selection, while a beta value smaller than alpha signifies negative selection. "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site Alpha Beta P-value Lineage Method

The FUBAR method within the HyPhy software was employed to analyze both positive and negative selection. FUBAR: pervasive selection on large datasets.
Note: List of sites found to be under pervasive selection by FUBAR (prob > 0.95). A prob[alpha < beta] value exceeding 0.95 indicates positive selection, while a prob[alpha > beta] value exceeding 0.95 indicates negative selection. "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site Prob[alpha>beta] Prob[alpha<beta] Lineage Method




Alterations in protein physicochemical properties induced by mutation (5619C>T)

Understanding the alterations in protein physicochemical properties can reveal the evolutionary processes and adaptive changes of viruses
Note: ProtParam software was used for the analysis of physicochemical properties. Significant change threshold: A change exceeding 10% compared to the reference is considered a significant change. "GRAVY" is an abbreviation for "grand average of hydropathicity".

Group Protein name Molecular weight Theoretical PI Extinction coefficients Aliphatic index GRAVY




Alterations in protein stability induced by mutation (5619C>T)

The impact of mutations on protein stability directly or indirectly affects the biological characteristics, adaptability, and transmission capacity of the virus
Note: iMutant 2.0 was utilized to analyze the effects of mutations on protein stability. pH 7 and a temperature of 25°C are employed to replicate the in vitro environment. pH 7.4 and a temperature of 37°C are utilized to simulate the in vivo environment.

Mutation Protein name Mutation type Position ΔDDG Stability pH Temperature Condition




Impact on protein function induced by mutation (5619C>T)

The impact of mutations on protein function
Note: The MutPred2 software was used to predict the pathogenicity of a mutation and gives the molecular mechanism of pathogenicity. A score above 0.5 indicates an increased likelihood of pathogenicity. "Pr" is the abbreviation for "proportion. P" is the abbreviation for "p-value.

Mutation Protein name Mutation type Score Molecular mechanisms




Exploring mutation (5619C>T) distribution within intrinsically disordered protein regions

Intrinsically Disordered Proteins (IDPs) which refers to protein regions that have no unique 3D structure. In viral proteins, mutations in the disordered regions s are critical for immune evasion and antibody escape, suggesting potential additional implications for vaccines and monoclonal therapeutic strategies.
Note: The iupred3 software was utilized for analyzing IDPs. A score greater than 0.5 is considered indicative of an IDP. In the plot, "POS" represents the position of the mutation.





Alterations in enzyme cleavage sites induced by mutation (5619C>T)

Exploring the impact of mutations on the cleavage sites of 28 enzymes.
Note: The PeptideCutter software was used for detecting enzymes cleavage sites. The increased enzymes cleavage sites refer to the cleavage sites in the mutated protein that are added compared to the reference protein. Conversely, the decreased enzymes cleavage sites indicate the cleavage sites in the mutated protein that are reduced compared to the reference protein.

Mutation Protein name Genome position Enzyme name Increased cleavage sites Decreased cleavage sites




Impact of spike protein mutation (5619C>T) on antigenicity and immunogenicity

Investigating the impact of mutations on antigenicity and immunogenicity carries important implications for vaccine design and our understanding of immune responses.
Note: An absolute change greater than 0.0102 (three times the median across sites) in antigenicity score is considered significant. An absolute changegreater than 0.2754 (three times the median across sites) in immunogenicity score is considered significant. The VaxiJen tool was utilized for antigenicity analysis. The IEDB tool was used for immunogenicity analysis. Antigens with a prediction score of more than 0.4 for this tool are considered candidate antigens. MHC I immunogenicity score >0, indicating a higher probability to stimulate an immune response.

Group Protein name Protein region Antigenicity score Immunogenicity score




Impact of mutation (5619C>T) on viral transmissibility by the affinity between RBD and ACE2 receptor

Unraveling the impact of mutations on the interaction between the receptor binding domain (RBD) and ACE2 receptor using deep mutational scanning (DMS) experimental data to gain insights into their effects on viral transmissibility.
Note: The ΔBinding affinity represents the disparity between the binding affinity of a mutation and the reference binding affinity. A positive Δbinding affinity value (Δlog10(KD,app) > 0) signifies an increased affinity between RBD and ACE2 receptor due to the mutation. Conversely, a negative value (Δlog10(KD,app) < 0) indicates a reduced affinity between RBD and ACE2 receptor caused by the mutation. A p-value smaller than 0.05 indicates significance. "Ave mut bind" represents the average binding affinity of this mutation. "Ave ref bind" refers to the average binding affinity at a site without any mutation (reference binding affinity).

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Mutation Protein name Protein region Mutation Position Ave mut bind Ave ref bind ΔBinding affinity P-value Image


The interface between the receptor binding domain (RBD) and ACE2 receptor is depicted in the crystal structure 6JM0.
Note: The structure 6M0J encompasses the RBD range of 333 to 526. The binding sites (403-406, 408, 417, 439, 445-447, 449, 453, 455-456, 473-478, 484-498, and 500-506) on the RBD that interface with ACE2 are indicated in magenta. The binding sites on the RBD that have been identified through the interface footprints experiment. The ACE2 binding sites within the interface are shown in cyan, representing residues within 5Å proximity to the RBD binding sites. The mutation within the RBD range of 333 to 526 is depicted in red.

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        Show interface residues:





Impact of mutation (5619C>T) on immune escape by the affinity between RBD and antibody/serum

By utilizing experimental data from deep mutational scanning (DMS), we can uncover how mutations affect the interaction between the receptor binding domain (RBD) and antibodies/serum. This approach provides valuable insights into strategies for evading the host immune response.
Note: We considered a mutation to mediate strong escape if the escape score exceeded 0.1 (10% of the maximum score of 1). A total of 1,504 antibodies/serum data were collected for this analysis. "Condition name" refers to the name of the antibodies/serum. "Mut escape score" represents the escape score of the mutation in that specific condition. "Avg mut escape score" indicates the average escape score of the mutation site in that condition, considering the occurrence of this mutation and other mutations. Class 1 antibodies bind to an epitope only in the RBD “up” conformation, and are the most abundant. Class 2 antibodies bind to the RBD both in “up” and “down” conformations. Class 3 and class 4 antibodies both bind outside the ACE2 binding site. Class 3 antibodies bind the RBD in both the open and closed conformation, while class 4 antibodies bind only in the open conformation.

Mutation Condition name Condition type Condition subtype Condition year Mut escape score Avg mut escape score




Investigating the co-mutation patterns of mutation (5619C>T) across 2,735 viral lineages

Investigating the co-mutation patterns of SARS-CoV-2 across 2,735 viral lineages to unravel the cooperative effects of different mutations. In biological research, correlation analysis of mutation sites helps us understand whether there is a close relationship or interaction between certain mutations.
Note: The Spearman correlation coefficient is used to calculate the correlation between two mutations within each Pango lineage. Holm–Bonferroni method was used for multiple test adjustment. We retained mutation pairs with correlation values greater than 0.6 or less than -0.6 and Holm–Bonferroni corrected p-values less than 0.05.

Associated mutation ID DNA mutation Mutation type Protein name Protein mutation correlation coefficient Lineage
V3055 18113C>T missense_variant ORF1ab_pp1ab T6038I 6.08e-1 AY.29
V5697 35C>T missense_variant ORF10 T12M 7.78e-1 AY.29
V6073 1497C>T synonymous_variant ORF1ab_pp1a F499F 8.60e-1 AY.29
V6809 6930C>T synonymous_variant ORF1ab_pp1a T2310T 8.09e-1 AY.29
V7424 11820C>T synonymous_variant ORF1ab_pp1a T3940T 7.69e-1 AY.29
V7580 13077C>T synonymous_variant ORF1ab_pp1a D4359D 7.89e-1 AY.29
V8691 435C>T synonymous_variant S Y145Y 7.57e-1 AY.29
V2447 13166C>T missense_variant ORF1ab_pp1a P4389L 6.28e-1 AY.5
V7515 12585A>G synonymous_variant ORF1ab_pp1a R4195R 7.00e-1 BA.4.1
V1348 5561C>T missense_variant ORF1ab_pp1a T1854I 6.43e-1 P.1
V8042 16662T>C synonymous_variant ORF1ab_pp1ab H5554H 7.24e-1 AY.103
V4388 145G>T missense_variant ORF3a G49C 7.75e-1 AY.126
V1422 6071C>T missense_variant ORF1ab_pp1a S2024L 7.12e-1 AY.47
V7344 11298C>T synonymous_variant ORF1ab_pp1a C3766C 8.39e-1 AY.47
V9194 315T>C synonymous_variant ORF3a F105F 7.58e-1 BA.1.1.1
V6245 2616C>T synonymous_variant ORF1ab_pp1a A872A 7.00e-1 BA.1.15.1
V2770 15983C>T missense_variant ORF1ab_pp1ab A5328V 7.07e-1 A.23.1
V74 -56G>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 A.23.1
V8659 240T>C synonymous_variant S D80D 7.07e-1 A.2.5
V9167 177T>C synonymous_variant ORF3a A59A 7.07e-1 A.2.5
V1205 4634A>G missense_variant ORF1ab_pp1a H1545R 6.12e-1 AD.2
V5910 384T>C synonymous_variant ORF1ab_pp1a N128N 6.12e-1 AD.2
V2603 14236G>T missense_variant ORF1ab_pp1ab V4746L 7.07e-1 AY.101
V5146 187G>T missense_variant ORF8 D63Y 7.07e-1 AY.101
V9326 304C>T synonymous_variant M L102L 7.82e-1 AY.102
V260 421_429delAAGTCATTT conservative_inframe_deletion ORF1ab_pp1a K141_F143del 7.07e-1 AY.108
V5780 *4360G>A downstream_gene_variant S None 7.07e-1 AY.108
V8284 18423C>T synonymous_variant ORF1ab_pp1ab C6141C 7.07e-1 AY.108
V8432 19602T>C synonymous_variant ORF1ab_pp1ab N6534N 7.07e-1 AY.108
V7597 13167C>T synonymous_variant ORF1ab_pp1a P4389P 1.00e+0 AY.109
V5424 544G>T missense_variant N A182S 7.07e-1 AY.10
V5834 *4484G>A downstream_gene_variant S None 7.07e-1 AY.10
V6265 2772C>T synonymous_variant ORF1ab_pp1a F924F -7.07e-1 AY.10
V6448 4230A>G synonymous_variant ORF1ab_pp1a K1410K 7.07e-1 AY.10
V745 2345C>T missense_variant ORF1ab_pp1a P782L 7.07e-1 AY.10
V8899 2046G>T synonymous_variant S R682R 7.07e-1 AY.10
V3402 20466G>T missense_variant ORF1ab_pp1ab K6822N 6.32e-1 AY.111
V4133 2812C>T missense_variant S L938F 6.32e-1 AY.111
V6982 8397T>C synonymous_variant ORF1ab_pp1a H2799H 6.32e-1 AY.111
V4371 124C>T missense_variant ORF3a P42S 1.00e+0 AY.116.1
V2023 10069G>A missense_variant ORF1ab_pp1a A3357T 9.70e-1 AY.119.2
V4819 91T>C missense_variant ORF6 Y31H 6.82e-1 AY.119
V4389 146G>T missense_variant ORF3a G49V 6.32e-1 AY.120.1
V7435 11874T>C synonymous_variant ORF1ab_pp1a A3958A 7.56e-1 AY.120.1
V8296 18492G>T synonymous_variant ORF1ab_pp1ab P6164P 7.56e-1 AY.120.1
V141 111G>T missense_variant ORF1ab_pp1a E37D 7.95e-1 AY.121
V1867 8707A>G missense_variant ORF1ab_pp1a I2903V 8.61e-1 AY.121
V1872 8726C>T missense_variant ORF1ab_pp1a A2909V 7.83e-1 AY.121
V4157 3080C>G missense_variant S T1027S 8.96e-1 AY.121
V5543 808G>T missense_variant N V270L 8.41e-1 AY.121
V6818 7014C>T synonymous_variant ORF1ab_pp1a F2338F 8.47e-1 AY.121
V8324 18682C>T synonymous_variant ORF1ab_pp1ab L6228L 8.81e-1 AY.121
V295 551G>A missense_variant ORF1ab_pp1a R184H 1.00e+0 AY.122.4
V5410 497C>T missense_variant N T166I 1.00e+0 AY.122.5
V2979 17629G>T missense_variant ORF1ab_pp1ab A5877S 7.06e-1 AY.123
V4090 2480C>T missense_variant S T827I 1.00e+0 AY.124
V8867 1869T>C synonymous_variant S A623A 9.12e-1 AY.131
V4610 719C>T missense_variant ORF3a P240L 7.07e-1 AY.16
V5977 795C>T synonymous_variant ORF1ab_pp1a T265T 7.07e-1 AY.16
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 7.07e-1 AY.16
V1036 3563C>T missense_variant ORF1ab_pp1a S1188L 8.56e-1 AY.1
V2672 15013C>T missense_variant ORF1ab_pp1ab H5005Y 6.82e-1 AY.1
V2901 17024C>T missense_variant ORF1ab_pp1ab T5675I 8.59e-1 AY.1
V4769 292G>T missense_variant M A98S 8.68e-1 AY.1
V7964 16044C>T synonymous_variant ORF1ab_pp1ab F5348F 7.07e-1 AY.25.3
V4264 3687G>T missense_variant S M1229I 6.32e-1 AY.3.1
V2332 12203C>T missense_variant ORF1ab_pp1a A4068V 7.56e-1 AY.34.1
V3870 1331A>G missense_variant S K444R 8.45e-1 AY.34.1
V2616 14357C>T missense_variant ORF1ab_pp1ab T4786M 7.74e-1 AY.34.2
V3992 1939G>T missense_variant S A647S 8.36e-1 AY.34.2
V5078 29T>C missense_variant ORF8 I10T 7.07e-1 AY.34
V5372 359G>T missense_variant N G120V 7.07e-1 AY.34
V1359 5669C>T missense_variant ORF1ab_pp1a T1890I 7.14e-1 AY.35
V281 496A>G missense_variant ORF1ab_pp1a S166G 7.71e-1 AY.35
V4846 -1C>T upstream_gene_variant ORF7a None 7.14e-1 AY.35
V530 1547C>T missense_variant ORF1ab_pp1a A516V 7.17e-1 AY.35
V7269 10569C>T synonymous_variant ORF1ab_pp1a A3523A 7.07e-1 AY.36.1
V1441 6136C>T missense_variant ORF1ab_pp1a P2046S 8.08e-1 AY.36
V7269 10569C>T synonymous_variant ORF1ab_pp1a A3523A 8.55e-1 AY.36
V4332 68C>T missense_variant ORF3a A23V 9.16e-1 AY.37
V5030 58C>T missense_variant ORF7b L20F 9.19e-1 AY.37
V6753 6441C>T synonymous_variant ORF1ab_pp1a N2147N 9.20e-1 AY.37
V8036 16623C>T synonymous_variant ORF1ab_pp1ab Y5541Y 9.56e-1 AY.37
V3781 761C>T missense_variant S S254F 7.07e-1 AY.4.10
V5544 812C>T missense_variant N T271I 7.07e-1 AY.4.10
V5216 352T>G missense_variant ORF8 L118V 7.07e-1 AY.4.11
V7925 15696C>T synonymous_variant ORF1ab_pp1ab A5232A 7.07e-1 AY.4.11
V2525 13689A>G missense_variant ORF1ab_pp1ab I4563M 7.07e-1 AY.4.12
V4823 98T>C missense_variant ORF6 I33T 1.00e+0 AY.4.12
V4973 286C>T missense_variant ORF7a L96F 7.07e-1 AY.4.12
V5729 *4312C>T downstream_gene_variant S None 1.00e+0 AY.4.12
V5941 570C>T synonymous_variant ORF1ab_pp1a F190F 8.16e-1 AY.4.12
V7094 9237C>T synonymous_variant ORF1ab_pp1a A3079A 7.07e-1 AY.4.12
V7645 13623C>T synonymous_variant ORF1ab_pp1ab Y4541Y 7.07e-1 AY.4.12
V8903 2076C>T synonymous_variant S I692I 8.16e-1 AY.4.12
V9654 471C>T synonymous_variant N I157I 1.00e+0 AY.4.12
V1101 3848C>T missense_variant ORF1ab_pp1a A1283V 6.32e-1 AY.4.13
V7410 11748T>C synonymous_variant ORF1ab_pp1a S3916S 1.00e+0 AY.4.13
V8795 1281T>C synonymous_variant S D427D 6.32e-1 AY.4.13
V1258 4910C>T missense_variant ORF1ab_pp1a T1637I 1.00e+0 AY.4.17
V2039 10193C>T missense_variant ORF1ab_pp1a T3398I 7.07e-1 AY.4.17
V3078 18227C>T missense_variant ORF1ab_pp1ab P6076L 7.07e-1 AY.43.3
V445 1192C>T missense_variant ORF1ab_pp1a R398C 1.00e+0 AY.43.9
V6336 3297G>A synonymous_variant ORF1ab_pp1a V1099V 1.00e+0 AY.43.9
V572 1678C>T missense_variant ORF1ab_pp1a R560C 1.00e+0 AY.46.3
V4176 3232G>T missense_variant S A1078S 8.16e-1 AY.48
V5222 357_358insCTG conservative_inframe_insertion ORF8 D119_F120insL 7.07e-1 AY.48
V5228 361delA frameshift_variant ORF8 I121fs 7.07e-1 AY.48
V1219 4700C>T missense_variant ORF1ab_pp1a T1567I 9.06e-1 AY.4.9
V1836 8549C>T missense_variant ORF1ab_pp1a A2850V 9.70e-1 AY.4.9
V4456 285G>T missense_variant ORF3a L95F 6.57e-1 AY.4.9
V6846 7299C>T synonymous_variant ORF1ab_pp1a S2433S 1.00e+0 AY.5.3
V2031 10111C>T missense_variant ORF1ab_pp1a P3371S 6.66e-1 AY.53
V3559 86C>T missense_variant S T29I 6.66e-1 AY.53
V6777 6703C>T synonymous_variant ORF1ab_pp1a L2235L 6.66e-1 AY.53
V7695 13995T>C synonymous_variant ORF1ab_pp1ab Y4665Y 8.16e-1 AY.53
V7388 11601C>T synonymous_variant ORF1ab_pp1a C3867C 6.74e-1 AY.54
V7695 13995T>C synonymous_variant ORF1ab_pp1ab Y4665Y 6.84e-1 AY.54
V2370 12485C>T missense_variant ORF1ab_pp1a A4162V 8.52e-1 AY.7.1
V3788 773G>T missense_variant S W258L 8.67e-1 AY.7.1
V4281 3754T>C missense_variant S S1252P 6.12e-1 AY.7.1
V5111 106C>T missense_variant ORF8 P36S 9.73e-1 AY.7.1
V8425 19557A>G synonymous_variant ORF1ab_pp1ab P6519P 9.73e-1 AY.7.1
V8595 21000T>C synonymous_variant ORF1ab_pp1ab S7000S 1.00e+0 AY.74
V2855 16748C>T missense_variant ORF1ab_pp1ab S5583L 8.16e-1 AY.81
V9257 816C>T synonymous_variant ORF3a S272S 1.00e+0 AY.81
V9800 1167G>A synonymous_variant N Q389Q 8.66e-1 AY.90
V1088 3745C>T missense_variant ORF1ab_pp1a L1249F 7.11e-1 AY.91
V1443 6139G>T missense_variant ORF1ab_pp1a V2047F 6.35e-1 AY.91
V3105 18413G>T missense_variant ORF1ab_pp1ab R6138L 6.35e-1 AY.91
V5082 37G>A missense_variant ORF8 V13I 6.65e-1 AY.91
V8326 18693T>C synonymous_variant ORF1ab_pp1ab N6231N 7.02e-1 AY.91
V443 1184C>T missense_variant ORF1ab_pp1a T395I 6.02e-1 AY.92
V9072 3417T>C synonymous_variant S D1139D 1.00e+0 B.1.110.3
V2001 9936G>T missense_variant ORF1ab_pp1a M3312I 6.31e-1 B.1.1.10
V3220 19261G>T missense_variant ORF1ab_pp1ab D6421Y 8.94e-1 B.1.1.10
V4436 229G>A missense_variant ORF3a V77I 8.94e-1 B.1.1.10
V5902 336C>T synonymous_variant ORF1ab_pp1a G112G 8.94e-1 B.1.1.10
V5997 921G>A synonymous_variant ORF1ab_pp1a A307A 8.94e-1 B.1.1.10
V7126 9538C>T synonymous_variant ORF1ab_pp1a L3180L 8.94e-1 B.1.1.10
V7943 15847C>T synonymous_variant ORF1ab_pp1ab L5283L 7.99e-1 B.1.1.10
V818 2739G>T missense_variant ORF1ab_pp1a E913D 8.94e-1 B.1.1.10
V9482 327T>C synonymous_variant ORF7a F109F 8.94e-1 B.1.1.10
V1980 9731C>T missense_variant ORF1ab_pp1a S3244L 7.07e-1 B.1.111
V4337 77C>T missense_variant ORF3a S26L 7.07e-1 B.1.111
V5479 626G>A missense_variant N R209K 7.07e-1 B.1.111
V5656 1250C>T missense_variant N T417I 7.07e-1 B.1.111
V7644 13596C>T synonymous_variant ORF1ab_pp1ab D4532D 7.07e-1 B.1.111
V80 -47G>A upstream_gene_variant ORF1ab_pp1a None 7.07e-1 B.1.111
V5642 1195G>T missense_variant N D399Y 8.65e-1 B.1.1.170
V2975 17558C>T missense_variant ORF1ab_pp1ab P5853L 1.00e+0 B.1.1.176
V9372 492G>T synonymous_variant M L164L 6.65e-1 B.1.1.189
V619 1841C>T missense_variant ORF1ab_pp1a T614I 6.57e-1 B.1.1.214
V3273 19691C>T missense_variant ORF1ab_pp1ab T6564I 6.55e-1 B.1.1.222
V706 2203G>A missense_variant ORF1ab_pp1a A735T 6.08e-1 B.1.1.222
V3060 18131C>T missense_variant ORF1ab_pp1ab A6044V 6.66e-1 B.1.1.25
V6446 4191C>T synonymous_variant ORF1ab_pp1a A1397A 8.16e-1 B.1.1.25
V9781 1074C>T synonymous_variant N D358D 1.00e+0 B.1.1.25
V4320 53G>A missense_variant ORF3a G18D 7.07e-1 B.1.1.263
V1928 9214G>T missense_variant ORF1ab_pp1a G3072C 1.00e+0 B.1.1.279
V3447 20813C>T missense_variant ORF1ab_pp1ab T6938I 1.00e+0 B.1.1.279
V2412 12817G>T missense_variant ORF1ab_pp1a A4273S 7.07e-1 B.1.1.284
V6185 2229G>A synonymous_variant ORF1ab_pp1a E743E 7.07e-1 B.1.1.284
V1225 4742C>T missense_variant ORF1ab_pp1a T1581M 8.45e-1 B.1.1.28
V5122 134G>T missense_variant ORF8 W45L 6.12e-1 B.1.1.28
V6061 1398C>T synonymous_variant ORF1ab_pp1a D466D 8.45e-1 B.1.1.28
V779 2576C>T missense_variant ORF1ab_pp1a A859V 1.00e+0 B.1.1.311
V3138 18664C>T missense_variant ORF1ab_pp1ab P6222S 7.07e-1 B.1.1.318
V4424 201G>T missense_variant ORF3a K67N 1.00e+0 B.1.1.318
V6669 5886C>T synonymous_variant ORF1ab_pp1a D1962D 1.00e+0 B.1.1.318
V4273 3711G>T missense_variant S M1237I 7.06e-1 B.1.1.326
V5950 613C>T synonymous_variant ORF1ab_pp1a L205L 7.06e-1 B.1.1.326
V6686 6006G>T synonymous_variant ORF1ab_pp1a T2002T 7.06e-1 B.1.1.326
V7623 13362T>C synonymous_variant ORF1ab_pp1ab D4454D 7.06e-1 B.1.1.326
V8269 18318C>T synonymous_variant ORF1ab_pp1ab V6106V 7.06e-1 B.1.1.326
V4986 314C>T missense_variant ORF7a A105V 8.16e-1 B.1.1.33
V8965 2571C>T synonymous_variant S G857G 8.16e-1 B.1.1.33
V9625 336C>T synonymous_variant N Y112Y 1.00e+0 B.1.139
V3036 17991G>T missense_variant ORF1ab_pp1ab M5997I 1.00e+0 B.1.1.416
V3962 1749G>T missense_variant S E583D 7.07e-1 B.1.1.416
V4892 113G>T missense_variant ORF7a G38V 9.55e-1 B.1.177.12
V5652 1238G>T missense_variant N S413I 8.69e-1 B.1.177.12
V2634 14565G>T missense_variant ORF1ab_pp1ab M4855I 6.06e-1 B.1.177.16
V3556 80C>T missense_variant S A27V 6.89e-1 B.1.177.16
V406 1049C>T missense_variant ORF1ab_pp1a T350I 1.00e+0 B.1.177.43
V4844 -4G>T upstream_gene_variant ORF7a None 1.00e+0 B.1.177.43
V7015 8613C>T synonymous_variant ORF1ab_pp1a G2871G 7.07e-1 B.1.177.43
V9123 3753A>G synonymous_variant S G1251G 7.07e-1 B.1.177.43
V7764 14448G>T synonymous_variant ORF1ab_pp1ab V4816V 6.75e-1 B.1.177.46
V3805 857C>T missense_variant S T286I 6.66e-1 B.1.177.60
V4483 322C>T missense_variant ORF3a L108F 6.66e-1 B.1.177.60
V7588 13116C>T synonymous_variant ORF1ab_pp1a V4372V 6.66e-1 B.1.177.60
V7744 14335C>T synonymous_variant ORF1ab_pp1ab L4779L 8.66e-1 B.1.177.60
V9378 537C>T synonymous_variant M Y179Y 8.66e-1 B.1.177.60
V6951 8103G>A synonymous_variant ORF1ab_pp1a A2701A 8.16e-1 B.1.177.62
V2311 11984C>T missense_variant ORF1ab_pp1a A3995V 6.32e-1 B.1.177.73
V2272 11766G>T missense_variant ORF1ab_pp1a Q3922H 6.46e-1 B.1.177.75
V2897 16995G>T missense_variant ORF1ab_pp1ab E5665D 6.67e-1 B.1.177.75
V7126 9538C>T synonymous_variant ORF1ab_pp1a L3180L 6.82e-1 B.1.177.75
V8036 16623C>T synonymous_variant ORF1ab_pp1ab Y5541Y 6.08e-1 B.1.177.75
V5106 94G>T missense_variant ORF8 V32L 7.07e-1 B.1.177.82
V1380 5804T>C missense_variant ORF1ab_pp1a I1935T 1.00e+0 B.1.177.83
V1494 6286A>G missense_variant ORF1ab_pp1a M2096V 1.00e+0 B.1.214.2
V1798 8341C>T missense_variant ORF1ab_pp1a L2781F 1.00e+0 B.1.214.2
V5915 414C>T synonymous_variant ORF1ab_pp1a A138A 1.00e+0 B.1.214.2
V8909 2145C>T synonymous_variant S P715P 9.13e-1 B.1.214.2
V9112 3645C>T synonymous_variant S Y1215Y 1.00e+0 B.1.214.2
V428 1127C>T missense_variant ORF1ab_pp1a S376L 6.21e-1 B.1.240
V5467 611G>T missense_variant N G204V 7.00e-1 B.1.240
V572 1678C>T missense_variant ORF1ab_pp1a R560C 6.78e-1 B.1.240
V616 1826C>T missense_variant ORF1ab_pp1a T609I 7.21e-1 B.1.240
V7168 9765C>T synonymous_variant ORF1ab_pp1a T3255T 7.84e-1 B.1.240
V7228 10242C>T synonymous_variant ORF1ab_pp1a N3414N 6.30e-1 B.1.240
V324 664A>G missense_variant ORF1ab_pp1a I222V 9.08e-1 B.1.241
V631 1879G>T missense_variant ORF1ab_pp1a V627F 6.14e-1 B.1.241
V6517 4734C>T synonymous_variant ORF1ab_pp1a N1578N 1.00e+0 B.1.258.14
V323 658G>A missense_variant ORF1ab_pp1a D220N 6.80e-1 B.1.258.17
V5106 94G>T missense_variant ORF8 V32L 8.16e-1 B.1.258.17
V7538 12754C>T synonymous_variant ORF1ab_pp1a L4252L 6.17e-1 B.1.258.17
V3009 17851C>T missense_variant ORF1ab_pp1ab H5951Y 1.00e+0 B.1.349
V6347 3357C>T synonymous_variant ORF1ab_pp1a G1119G 1.00e+0 B.1.349
V7677 13854G>T synonymous_variant ORF1ab_pp1ab T4618T 1.00e+0 B.1.349
V805 2674C>T missense_variant ORF1ab_pp1a P892S 1.00e+0 B.1.349
V2188 11152G>T missense_variant ORF1ab_pp1a V3718F 7.07e-1 B.1.351.3
V5644 1204G>T missense_variant N D402Y 7.07e-1 B.1.351.3
V2484 13447A>G missense_variant ORF1ab_pp1ab K4483E 1.00e+0 B.1.356
V3526 35C>T missense_variant S S12F 1.00e+0 B.1.356
V5437 572G>T missense_variant N R191L 1.00e+0 B.1.356
V5952 639C>T synonymous_variant ORF1ab_pp1a C213C 7.06e-1 B.1.356
V4015 2031G>T missense_variant S Q677H 6.10e-1 B.1.36.16
V6116 1797C>T synonymous_variant ORF1ab_pp1a A599A 6.69e-1 B.1.36.16
V8715 645T>C synonymous_variant S D215D 6.69e-1 B.1.36.16
V9338 351C>T synonymous_variant M N117N 8.65e-1 B.1.36.16
V3079 18234G>T missense_variant ORF1ab_pp1ab M6078I 1.00e+0 B.1.36.17
V9171 192C>T synonymous_variant ORF3a T64T 1.00e+0 B.1.36.17
V9813 1245C>T synonymous_variant N D415D 1.00e+0 B.1.36.17
V354 848C>T missense_variant ORF1ab_pp1a T283I 6.32e-1 B.1.36.29
V5916 418C>T synonymous_variant ORF1ab_pp1a L140L 6.32e-1 B.1.36.29
V260 421_429delAAGTCATTT conservative_inframe_deletion ORF1ab_pp1a K141_F143del 7.06e-1 B.1.36.31
V375 920C>T missense_variant ORF1ab_pp1a A307V 1.00e+0 B.1.36.31
V8838 1644C>T synonymous_variant S G548G 1.00e+0 B.1.36.31
V8887 1995C>T synonymous_variant S P665P 1.00e+0 B.1.36.31
V8964 2568C>T synonymous_variant S N856N 1.00e+0 B.1.36.31
V438 1162C>T missense_variant ORF1ab_pp1a H388Y 7.45e-1 B.1.369
V5014 14C>T missense_variant ORF7b S5L 6.27e-1 B.1.369
V1181 4519C>T missense_variant ORF1ab_pp1a L1507F 1.00e+0 B.1.396
V4101 2534C>T missense_variant S A845V 7.07e-1 B.1.396
V4854 22G>A missense_variant ORF7a A8T 7.07e-1 B.1.396
V5794 *4371G>T downstream_gene_variant S None 7.07e-1 B.1.396
V4328 64G>C missense_variant ORF3a D22H 1.00e+0 B.1.400
V4797 5T>C missense_variant ORF6 F2S 1.00e+0 B.1.400
V5464 610G>A missense_variant N G204R 1.00e+0 B.1.400
V5614 1129G>T missense_variant N D377Y 7.07e-1 B.1.400
V5841 48C>T synonymous_variant ORF1ab_pp1a L16L 7.07e-1 B.1.400
V2857 16755G>T missense_variant ORF1ab_pp1ab E5585D 8.16e-1 B.1.426
V3592 224G>T missense_variant S G75V 8.16e-1 B.1.426
V1144 4202C>T missense_variant ORF1ab_pp1a T1401I 1.00e+0 B.1.428
V1206 4639G>T missense_variant ORF1ab_pp1a D1547Y 1.00e+0 B.1.428
V460 1249C>T missense_variant ORF1ab_pp1a H417Y 1.00e+0 B.1.428
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 1.00e+0 B.1.428
V7872 15315C>T synonymous_variant ORF1ab_pp1ab N5105N 1.00e+0 B.1.428
V7892 15474C>T synonymous_variant ORF1ab_pp1ab F5158F 7.07e-1 B.1.428
V1111 3901A>G missense_variant ORF1ab_pp1a I1301V 7.89e-1 B.1.438.1
V2334 12223C>T missense_variant ORF1ab_pp1a P4075S 9.48e-1 B.1.438.1
V3036 17991G>T missense_variant ORF1ab_pp1ab M5997I 7.53e-1 B.1.438.1
V4500 379C>T missense_variant ORF3a L127F 6.78e-1 B.1.438.1
V8036 16623C>T synonymous_variant ORF1ab_pp1ab Y5541Y 6.67e-1 B.1.438.1
V9504 6A>G synonymous_variant ORF8 K2K 7.59e-1 B.1.438.1
V2228 11330A>G missense_variant ORF1ab_pp1a Q3777R 8.00e-1 B.1.466.2
V2582 14029C>T missense_variant ORF1ab_pp1ab R4677C 8.21e-1 B.1.466.2
V2653 14762C>T missense_variant ORF1ab_pp1ab A4921V 6.93e-1 B.1.466.2
V2897 16995G>T missense_variant ORF1ab_pp1ab E5665D 7.49e-1 B.1.466.2
V2905 17067G>T missense_variant ORF1ab_pp1ab E5689D 8.21e-1 B.1.466.2
V4687 184G>T missense_variant E V62F 7.19e-1 B.1.466.2
V5969 723C>T synonymous_variant ORF1ab_pp1a Y241Y 8.21e-1 B.1.466.2
V7119 9480C>T synonymous_variant ORF1ab_pp1a Y3160Y 8.21e-1 B.1.466.2
V9304 159C>T synonymous_variant M F53F 7.19e-1 B.1.466.2
V3387 20314G>T missense_variant ORF1ab_pp1ab V6772L 1.00e+0 B.1.497
V1111 3901A>G missense_variant ORF1ab_pp1a I1301V 1.00e+0 B.1.509
V5509 688C>T missense_variant N L230F 1.00e+0 B.1.509
V7562 12951T>C synonymous_variant ORF1ab_pp1a D4317D 1.00e+0 B.1.509
V7042 8853C>T synonymous_variant ORF1ab_pp1a D2951D 7.07e-1 B.1.517
V7067 9015A>G synonymous_variant ORF1ab_pp1a V3005V 7.07e-1 B.1.517
V7423 11811C>T synonymous_variant ORF1ab_pp1a N3937N 7.07e-1 B.1.517
V7448 12003G>A synonymous_variant ORF1ab_pp1a L4001L 7.07e-1 B.1.525
V3080 18244C>T missense_variant ORF1ab_pp1ab L6082F 7.07e-1 B.1.560
V5136 164C>T missense_variant ORF8 A55V 1.00e+0 B.1.560
V6065 1431G>A synonymous_variant ORF1ab_pp1a L477L 1.00e+0 B.1.560
V6092 1635A>G synonymous_variant ORF1ab_pp1a R545R 1.00e+0 B.1.560
V7602 13194G>T synonymous_variant ORF1ab_pp1a S4398S 1.00e+0 B.1.560
V4916 182C>T missense_variant ORF7a T61I 1.00e+0 B.1.564
V1219 4700C>T missense_variant ORF1ab_pp1a T1567I 6.11e-1 B.1.568
V1810 8390C>T missense_variant ORF1ab_pp1a S2797F 6.30e-1 B.1.568
V1920 9166G>A missense_variant ORF1ab_pp1a V3056I 6.32e-1 B.1.575
V2900 17021C>T missense_variant ORF1ab_pp1ab S5674L 7.74e-1 B.1.575
V6577 5127C>T synonymous_variant ORF1ab_pp1a N1709N 6.70e-1 B.1.575
V8534 20542C>T synonymous_variant ORF1ab_pp1ab L6848L 6.70e-1 B.1.575
V8630 75C>T synonymous_variant S P25P 7.74e-1 B.1.575
V1796 8332C>T missense_variant ORF1ab_pp1a L2778F 7.07e-1 B.1.582
V2160 11022_11030delGTCTGGTTT disruptive_inframe_deletion ORF1ab_pp1a L3674_G3676del 1.00e+0 B.1.582
V5435 568A>G missense_variant N S190G 1.00e+0 B.1.582
V6029 1176C>T synonymous_variant ORF1ab_pp1a G392G 7.07e-1 B.1.582
V6419 3990G>A synonymous_variant ORF1ab_pp1a P1330P 7.07e-1 B.1.582
V1347 5557C>T missense_variant ORF1ab_pp1a L1853F 8.94e-1 B.1.609
V1022 3503C>T missense_variant ORF1ab_pp1a T1168I 1.00e+0 B.1.621.2
V1812 8395C>T missense_variant ORF1ab_pp1a H2799Y 7.07e-1 B.1.621.2
V3126 18595G>T missense_variant ORF1ab_pp1ab A6199S 1.00e+0 B.1.621.2
V4523 463G>C missense_variant ORF3a D155H 7.07e-1 B.1.621.2
V5357 268G>T missense_variant N A90S 1.00e+0 B.1.621.2
V8206 17865C>T synonymous_variant ORF1ab_pp1ab D5955D 1.00e+0 B.1.621.2
V5160 200C>T missense_variant ORF8 S67F 6.67e-1 B.1.637
V6870 7503C>T synonymous_variant ORF1ab_pp1a I2501I 7.01e-1 B.1.637
V1128 4031C>T missense_variant ORF1ab_pp1a T1344I 1.00e+0 B.4
V8158 17481C>T synonymous_variant ORF1ab_pp1ab N5827N 1.00e+0 B.4
V842 2831C>T missense_variant ORF1ab_pp1a S944L 1.00e+0 B.4
V8569 20859G>T synonymous_variant ORF1ab_pp1ab G6953G 1.00e+0 B.4
V7304 10908C>T synonymous_variant ORF1ab_pp1a L3636L 1.00e+0 BA.1.1.12
V2152 10987A>G missense_variant ORF1ab_pp1a I3663V 7.42e-1 BA.1.1.14
V1590 6778C>T missense_variant ORF1ab_pp1a P2260S 6.61e-1 BA.1.1.15
V855 2888G>A missense_variant ORF1ab_pp1a G963D 6.32e-1 BA.1.13.1
V8218 17982C>T synonymous_variant ORF1ab_pp1ab Y5994Y 7.07e-1 BA.1.1.4
V496 1351C>A missense_variant ORF1ab_pp1a L451I 7.07e-1 BA.1.14
V6263 2757T>C synonymous_variant ORF1ab_pp1a H919H 7.07e-1 BA.1.14
V119 35C>T missense_variant ORF1ab_pp1a T12I 1.00e+0 BA.1.15.2
V865 2914G>A missense_variant ORF1ab_pp1a E972K 1.00e+0 BA.1.15.2
V4367 121C>T missense_variant ORF3a L41F 6.54e-1 BA.1.16
V5009 7G>A missense_variant ORF7b E3K 6.54e-1 BA.1.16
V5409 494C>T missense_variant N T165I 1.00e+0 BA.1.21.1
V6493 4567C>T synonymous_variant ORF1ab_pp1a L1523L 6.32e-1 BA.2.12
V9341 363C>T synonymous_variant M N121N 8.09e-1 BA.2.13
V5170 216G>T missense_variant ORF8 Q72H 8.59e-1 BA.2.18
V5726 *4304G>T downstream_gene_variant S None 6.02e-1 BA.2.18
V8662 249C>T synonymous_variant S V83V 7.10e-1 BA.2.18
V7511 12558C>T synonymous_variant ORF1ab_pp1a S4186S 1.00e+0 BA.2.19
V323 658G>A missense_variant ORF1ab_pp1a D220N 7.07e-1 BA.2.23
V2317 12047C>T missense_variant ORF1ab_pp1a A4016V 6.32e-1 BA.2.24
V8182 17670C>T synonymous_variant ORF1ab_pp1ab T5890T 7.07e-1 BA.2.2
V8285 18429C>T synonymous_variant ORF1ab_pp1ab S6143S 8.16e-1 BA.2.3.11
V850 2857G>T missense_variant ORF1ab_pp1a D953Y 1.00e+0 BA.2.3.11
V3881 1345T>C missense_variant S Y449H 6.54e-1 BA.2.3.13
V7052 8901C>T synonymous_variant ORF1ab_pp1a T2967T 6.32e-1 BA.2.3.1
V8345 18852A>G synonymous_variant ORF1ab_pp1ab K6284K 7.07e-1 BA.2.31
V8603 21078C>T synonymous_variant ORF1ab_pp1ab Y7026Y 7.07e-1 BA.2.31
V9445 153T>C synonymous_variant ORF7a D51D 6.75e-1 BA.2.3.20
V4141 2837G>T missense_variant S G946V 1.00e+0 BA.2.3.2
V6225 2490G>T synonymous_variant ORF1ab_pp1a V830V 7.07e-1 BA.2.3.2
V6689 6021C>T synonymous_variant ORF1ab_pp1a T2007T 7.07e-1 BA.2.3.2
V8032 16584C>T synonymous_variant ORF1ab_pp1ab D5528D 1.00e+0 BA.2.3.2
V2898 17003A>G missense_variant ORF1ab_pp1ab D5668G 8.99e-1 BA.2.36
V3454 20873A>G missense_variant ORF1ab_pp1ab K6958R 8.20e-1 BA.2.36
V3767 742T>C missense_variant S Y248H 8.88e-1 BA.2.36
V4076 2372C>T missense_variant S T791I 9.41e-1 BA.2.36
V6147 1998C>A synonymous_variant ORF1ab_pp1a T666T 7.70e-1 BA.2.36
V7830 14976C>T synonymous_variant ORF1ab_pp1ab N4992N 7.90e-1 BA.2.38
V2368 12482C>T missense_variant ORF1ab_pp1a T4161I 8.16e-1 BA.2.40.1
V9289 33A>G synonymous_variant M E11E 8.16e-1 BA.2.56
V4721 11C>T missense_variant M S4F 7.07e-1 BA.2.65
V6876 7566T>C synonymous_variant ORF1ab_pp1a V2522V 7.07e-1 BA.2.65
V6362 3522C>T synonymous_variant ORF1ab_pp1a Y1174Y 1.00e+0 BA.2.68
V5257 20A>G missense_variant N Q7R 1.00e+0 BA.2.72
V4683 172G>A missense_variant E V58I 1.00e+0 BA.2.74
V9783 1080C>T synonymous_variant N Y360Y 7.07e-1 BA.2.75.2
V2444 13160G>A missense_variant ORF1ab_pp1a R4387H 7.07e-1 BA.2.75.3
V4937 220G>T missense_variant ORF7a V74F 7.07e-1 BA.2.75.3
V6340 3327T>C synonymous_variant ORF1ab_pp1a N1109N 7.07e-1 BA.2.75.3
V8991 2808C>T synonymous_variant S D936D 7.07e-1 BA.2.75.3
V6053 1341T>C synonymous_variant ORF1ab_pp1a N447N 7.07e-1 BA.2.75
V1152 4286C>T missense_variant ORF1ab_pp1a T1429I 8.66e-1 BA.2.76
V8001 16311C>T synonymous_variant ORF1ab_pp1ab D5437D 6.12e-1 BA.2.76
V3052 18065C>T missense_variant ORF1ab_pp1ab T6022I 1.00e+0 BA.2.9.3
V4486 329C>T missense_variant ORF3a A110V 7.06e-1 BA.4.1.9
V5598 1090C>T missense_variant N P364S 7.07e-1 BA.4.2
V6466 4365T>C synonymous_variant ORF1ab_pp1a H1455H 7.07e-1 BA.4.2
V7844 15102T>C synonymous_variant ORF1ab_pp1ab H5034H 6.32e-1 BA.4.6.4
V5176 229G>T missense_variant ORF8 G77C 7.07e-1 BA.4.7
V5636 1174G>T missense_variant N V392L 6.75e-1 BA.5.1.10
V8451 19752C>T synonymous_variant ORF1ab_pp1ab D6584D 7.06e-1 BA.5.1.11
V3168 18837G>T missense_variant ORF1ab_pp1ab Q6279H 8.58e-1 BA.5.1.12
V6247 2637C>T synonymous_variant ORF1ab_pp1a V879V 7.99e-1 BA.5.1.12
V9659 486T>C synonymous_variant N P162P 8.27e-1 BA.5.1.12
V9117 3690G>T synonymous_variant S V1230V 6.03e-1 BA.5.1.23
V2559 13919C>T missense_variant ORF1ab_pp1ab T4640I 6.97e-1 BA.5.1.26
V3710 554A>G missense_variant S N185S 8.12e-1 BA.5.1.26
V1320 5407C>T missense_variant ORF1ab_pp1a P1803S 8.66e-1 BA.5.1.6
V4366 119C>T missense_variant ORF3a S40L 6.70e-1 BA.5.1.6
V9388 606C>T synonymous_variant M G202G 1.00e+0 BA.5.1.8
V5904 348G>A synonymous_variant ORF1ab_pp1a V116V 6.73e-1 BA.5.2.13
V6507 4662C>T synonymous_variant ORF1ab_pp1a D1554D 6.70e-1 BA.5.2.13
V1450 6154G>T missense_variant ORF1ab_pp1a V2052L 1.00e+0 BA.5.2.27
V6474 4386T>C synonymous_variant ORF1ab_pp1a A1462A 7.07e-1 BA.5.2.27
V7682 13914C>T synonymous_variant ORF1ab_pp1ab T4638T 8.66e-1 BA.5.2.27
V7885 15414C>T synonymous_variant ORF1ab_pp1ab Y5138Y 8.66e-1 BA.5.2.27
V6019 1077C>T synonymous_variant ORF1ab_pp1a Y359Y 1.00e+0 BA.5.2.28
V1784 8275G>A missense_variant ORF1ab_pp1a A2759T 9.70e-1 BA.5.2.34
V7755 14385C>T synonymous_variant ORF1ab_pp1ab N4795N 9.64e-1 BA.5.2.34
V9316 231C>T synonymous_variant M T77T 9.12e-1 BA.5.2.34
V9405 90T>C synonymous_variant ORF6 D30D 6.86e-1 BA.5.2.34
V1856 8624G>A missense_variant ORF1ab_pp1a R2875H 1.00e+0 BA.5.2.43
V1511 6368C>T missense_variant ORF1ab_pp1a A2123V 8.66e-1 BA.5.2.49
V5129 152C>T missense_variant ORF8 A51V 1.00e+0 BA.5.2.49
V7744 14335C>T synonymous_variant ORF1ab_pp1ab L4779L 7.49e-1 BA.5.2.49
V1721 7825C>T missense_variant ORF1ab_pp1a L2609F 7.07e-1 BA.5.3.3
V3739 643G>C missense_variant S D215H 7.07e-1 BA.5.3.3
V9233 666C>T synonymous_variant ORF3a D222D 7.07e-1 BA.5.3.3
V3272 19687C>T missense_variant ORF1ab_pp1ab P6563S 8.16e-1 BA.5.5.1
V6219 2445C>T synonymous_variant ORF1ab_pp1a L815L 9.13e-1 BA.5.5.1
V6384 3747C>T synonymous_variant ORF1ab_pp1a L1249L 9.13e-1 BA.5.5.1
V7819 14877C>T synonymous_variant ORF1ab_pp1ab T4959T 8.16e-1 BA.5.5.1
V3099 18383C>T missense_variant ORF1ab_pp1ab P6128L 1.00e+0 BA.5.6.2
V427 1120C>T missense_variant ORF1ab_pp1a H374Y 1.00e+0 BA.5.6.2
V3870 1331A>G missense_variant S K444R 1.00e+0 BA.5.7
V8071 16866C>T synonymous_variant ORF1ab_pp1ab Y5622Y 9.58e-1 BE.1.1.1
V992 3373G>T missense_variant ORF1ab_pp1a G1125C 7.07e-1 BE.1.2
V3009 17851C>T missense_variant ORF1ab_pp1ab H5951Y 1.00e+0 BE.1.4
V561 1648C>T missense_variant ORF1ab_pp1a R550C 7.07e-1 BE.1.4
V5666 -15G>T upstream_gene_variant ORF10 None 7.07e-1 BE.2
V6941 8034C>T synonymous_variant ORF1ab_pp1a N2678N 1.00e+0 BE.4.1
V4034 2063C>T missense_variant S A688V 7.74e-1 BE.5
V5335 146C>T missense_variant N T49I 7.06e-1 BF.11.5
V9777 1038C>T synonymous_variant N F346F 1.00e+0 BF.11.5
V921 3104C>T missense_variant ORF1ab_pp1a T1035I 6.06e-1 BF.11
V2211 11256G>T missense_variant ORF1ab_pp1a M3752I 7.07e-1 BF.25
V5097 82C>T missense_variant ORF8 H28Y 7.07e-1 BF.25
V8840 1668C>T synonymous_variant S N556N 7.07e-1 BF.25
V6461 4317C>T synonymous_variant ORF1ab_pp1a N1439N 1.00e+0 BF.31.1
V798 2645C>T missense_variant ORF1ab_pp1a T882I 1.00e+0 BF.32
V2649 14752G>T missense_variant ORF1ab_pp1ab A4918S 7.07e-1 BF.4
V9273 96C>T synonymous_variant E A32A 1.00e+0 BF.7.14
V155 146G>A missense_variant ORF1ab_pp1a G49D 6.66e-1 BF.7.4
V2082 10609A>G missense_variant ORF1ab_pp1a N3537D 1.00e+0 BF.7.5
V3411 20495C>T missense_variant ORF1ab_pp1ab A6832V 1.00e+0 BF.7.6
V3939 1640C>A missense_variant S T547K 1.00e+0 BF.7.6
V5224 358T>G missense_variant ORF8 F120V 1.00e+0 BF.7.6
V5230 361A>C missense_variant ORF8 I121L 7.07e-1 BF.7.6
V6201 2361G>A synonymous_variant ORF1ab_pp1a G787G 1.00e+0 BF.7.6
V7084 9165C>T synonymous_variant ORF1ab_pp1a I3055I 1.00e+0 BF.7.6
V8632 96C>T synonymous_variant S F32F 1.00e+0 BF.7.6
V9437 117A>G synonymous_variant ORF7a T39T 6.17e-1 BF.8
V9610 234C>T synonymous_variant N S78S 6.17e-1 BF.8
V593 1738C>T missense_variant ORF1ab_pp1a L580F 7.07e-1 BL.1
V7145 9642C>T synonymous_variant ORF1ab_pp1a Y3214Y 7.07e-1 BL.1
V6913 7827C>T synonymous_variant ORF1ab_pp1a L2609L 1.00e+0 BL.2
V223 331G>A missense_variant ORF1ab_pp1a V111M 1.00e+0 BM.1.1.3
V4521 452C>T missense_variant ORF3a T151I 1.00e+0 BM.1.1.3
V5477 623C>T missense_variant N A208V 7.07e-1 BM.1.1.3
V5075 23G>T missense_variant ORF8 G8V 7.07e-1 BM.4.1.1
V9229 636C>T synonymous_variant ORF3a Y212Y 7.07e-1 BM.4.1.1
V306 607G>A missense_variant ORF1ab_pp1a D203N 6.70e-1 BN.1.5
V7376 11517A>G synonymous_variant ORF1ab_pp1a K3839K 6.70e-1 BN.1.5
V7892 15474C>T synonymous_variant ORF1ab_pp1ab F5158F 1.00e+0 BN.1.9
V9380 552G>A synonymous_variant M S184S 1.00e+0 BN.1.9
V6735 6339A>G synonymous_variant ORF1ab_pp1a L2113L 1.00e+0 BN.1
V1304 5284C>T missense_variant ORF1ab_pp1a L1762F 6.06e-1 BQ.1.1.13
V1479 6248_6250delGTT disruptive_inframe_deletion ORF1ab_pp1a S2083_L2084delinsI 7.33e-1 BQ.1.1.13
V7251 10437C>T synonymous_variant ORF1ab_pp1a D3479D 7.85e-1 BQ.1.11
V7021 8682C>T synonymous_variant ORF1ab_pp1a N2894N 9.35e-1 BQ.1.1.20
V6579 5148C>T synonymous_variant ORF1ab_pp1a A1716A 6.66e-1 BQ.1.1.25
V8335 18765C>T synonymous_variant ORF1ab_pp1ab H6255H 7.36e-1 BQ.1.1.25
V8865 1854A>T synonymous_variant S T618T 8.88e-1 BQ.1.1.25
V4853 17T>C missense_variant ORF7a F6S 7.06e-1 BQ.1.1.27
V8649 201T>C synonymous_variant S A67A 7.06e-1 BQ.1.1.27
V8396 19260C>T synonymous_variant ORF1ab_pp1ab L6420L 6.66e-1 BQ.1.1.29
V8865 1854A>T synonymous_variant S T618T 6.72e-1 BQ.1.1.32
V445 1192C>T missense_variant ORF1ab_pp1a R398C 1.00e+0 BQ.1.13
V9806 1209C>T synonymous_variant N F403F 9.30e-1 BQ.1.15
V2178 11080C>T missense_variant ORF1ab_pp1a L3694F 7.06e-1 BQ.1.16
V5286 61T>C missense_variant N S21P 7.06e-1 BQ.1.16
V6332 3270C>T synonymous_variant ORF1ab_pp1a Y1090Y 6.32e-1 BQ.1.18
V6464 4353C>T synonymous_variant ORF1ab_pp1a G1451G 6.32e-1 BQ.1.18
V2178 11080C>T missense_variant ORF1ab_pp1a L3694F 9.32e-1 BQ.1.23
V5286 61T>C missense_variant N S21P 9.10e-1 BQ.1.23
V1873 8729C>T missense_variant ORF1ab_pp1a T2910I 8.25e-1 BQ.1.5
V5195 302G>A missense_variant ORF8 R101H 6.12e-1 BQ.1.8
V2178 11080C>T missense_variant ORF1ab_pp1a L3694F 8.52e-1 BQ.1
V5286 61T>C missense_variant N S21P 8.45e-1 BQ.1
V1152 4286C>T missense_variant ORF1ab_pp1a T1429I 1.00e+0 BW.1
V3720 620A>G missense_variant S H207R 1.00e+0 BY.1
V7062 8958C>T synonymous_variant ORF1ab_pp1a H2986H 1.00e+0 BY.1
V2829 16588G>T missense_variant ORF1ab_pp1ab G5530C 7.06e-1 C.16
V2965 17486C>T missense_variant ORF1ab_pp1ab A5829V 7.06e-1 C.16
V3468 20929G>T missense_variant ORF1ab_pp1ab D6977Y 8.65e-1 C.16
V7257 10476C>T synonymous_variant ORF1ab_pp1a D3492D 7.49e-1 C.16
V9348 385C>T synonymous_variant M L129L 6.69e-1 C.16
V1539 6461C>T missense_variant ORF1ab_pp1a T2154I 1.00e+0 C.35
V2472 13353G>T missense_variant ORF1ab_pp1ab K4451N 1.00e+0 C.35
V2587 14054C>T missense_variant ORF1ab_pp1ab T4685I 1.00e+0 C.35
V32 -126C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 C.35
V347 812C>T missense_variant ORF1ab_pp1a P271L 1.00e+0 C.35
V5088 55G>T stop_gained ORF8 E19* 7.07e-1 C.35
V5204 328G>T stop_gained ORF8 E110* 1.00e+0 C.35
V5980 822A>G synonymous_variant ORF1ab_pp1a V274V 1.00e+0 C.35
V6368 3567C>T synonymous_variant ORF1ab_pp1a S1189S 1.00e+0 C.35
V6538 4879C>T synonymous_variant ORF1ab_pp1a L1627L 1.00e+0 C.35
V9703 729C>A synonymous_variant N G243G 7.07e-1 C.35
V9647 444C>T synonymous_variant N T148T 1.00e+0 C.36
V1182 4523C>T missense_variant ORF1ab_pp1a A1508V 6.73e-1 C.37
V6910 7809C>T synonymous_variant ORF1ab_pp1a N2603N 6.88e-1 CH.1.1.3
V6910 7809C>T synonymous_variant ORF1ab_pp1a N2603N 8.16e-1 CH.1.1
V7353 11388C>T synonymous_variant ORF1ab_pp1a L3796L 7.07e-1 CK.1
V8583 20952C>T synonymous_variant ORF1ab_pp1ab H6984H 7.07e-1 CK.1
V9479 315G>A synonymous_variant ORF7a A105A 7.07e-1 CK.1
V1816 8419A>G missense_variant ORF1ab_pp1a I2807V 8.16e-1 CK.2.1.1
V9445 153T>C synonymous_variant ORF7a D51D 7.07e-1 CM.2
V1241 4790C>T missense_variant ORF1ab_pp1a T1597I 7.06e-1 DE.2
V2986 17713C>T missense_variant ORF1ab_pp1ab L5905F 1.00e+0 DF.1
V5636 1174G>T missense_variant N V392L 7.07e-1 DL.1
V1386 5836G>A missense_variant ORF1ab_pp1a G1946S 1.00e+0 P.1.13
V6412 3937C>T synonymous_variant ORF1ab_pp1a L1313L 1.00e+0 P.1.13
V1512 6371C>T missense_variant ORF1ab_pp1a T2124I 8.00e-1 P.1.15
V5564 931G>A missense_variant N A311T 7.52e-1 P.1.15
V1219 4700C>T missense_variant ORF1ab_pp1a T1567I 7.07e-1 P.1.17
V4273 3711G>T missense_variant S M1237I 7.74e-1 P.1.1
V567 1661C>T missense_variant ORF1ab_pp1a T554I 6.32e-1 P.1.2
V7253 10449C>T synonymous_variant ORF1ab_pp1a L3483L 8.94e-1 P.1.2
V7649 13665T>C synonymous_variant ORF1ab_pp1ab Y4555Y 6.32e-1 P.1.2
V8034 16605C>T synonymous_variant ORF1ab_pp1ab Y5535Y 6.32e-1 P.1.2
V905 3050C>T missense_variant ORF1ab_pp1a T1017I 6.32e-1 P.1.2
V9273 96C>T synonymous_variant E A32A 6.32e-1 P.1.2
V9568 48G>T synonymous_variant N T16T 6.32e-1 P.1.2
V1747 7963C>T missense_variant ORF1ab_pp1a L2655F 7.06e-1 P.1.7.1
V5576 980C>T missense_variant N S327L 8.32e-1 P.1.7.1
V8583 20952C>T synonymous_variant ORF1ab_pp1ab H6984H 9.12e-1 P.1.7.1
V6380 3727C>T synonymous_variant ORF1ab_pp1a L1243L 7.07e-1 Q.3
V7307 10959C>T synonymous_variant ORF1ab_pp1a V3653V 1.00e+0 Q.3
V3195 19000C>T missense_variant ORF1ab_pp1ab L6334F 1.00e+0 Q.4
V7291 10755C>T synonymous_variant ORF1ab_pp1a L3585L 7.07e-1 XAY.2
V8985 2775C>T synonymous_variant S N925N 7.07e-1 XAY.2
V2400 12659C>T missense_variant ORF1ab_pp1a P4220L 1.00e+0 XAZ
V7191 9924C>T synonymous_variant ORF1ab_pp1a T3308T 6.30e-1 XBB
V5974 756G>A synonymous_variant ORF1ab_pp1a Q252Q 6.32e-1 XBF
V783 2597C>T missense_variant ORF1ab_pp1a T866I 6.32e-1 XBF
V1451 6163C>T missense_variant ORF1ab_pp1a P2055S 6.12e-1 XB
V1813 8399C>T missense_variant ORF1ab_pp1a T2800I 1.00e+0 XBK
V3447 20813C>T missense_variant ORF1ab_pp1ab T6938I 6.99e-1 A.2.5.3
V3539 62G>C missense_variant S R21T 1.00e+0 A.2.5.3
V5617 1132G>C missense_variant N E378Q 6.99e-1 A.2.5.3
V6493 4567C>T synonymous_variant ORF1ab_pp1a L1523L 6.99e-1 A.2.5.3
V1131 4055C>T missense_variant ORF1ab_pp1a A1352V -8.29e-1 AM.2
V2183 11131C>T missense_variant ORF1ab_pp1a L3711F -8.29e-1 AM.2
V911 3063G>T missense_variant ORF1ab_pp1a Q1021H -6.12e-1 AM.2
V6572 5088A>G synonymous_variant ORF1ab_pp1a Q1696Q 1.00e+0 AY.124.1.1
V7363 11466T>C synonymous_variant ORF1ab_pp1a Y3822Y 7.06e-1 AY.124.1.1
V2745 15718G>T missense_variant ORF1ab_pp1ab V5240L 7.05e-1 AY.133
V4134 2816C>T missense_variant S S939F 1.00e+0 AY.133
V454 1208C>T missense_variant ORF1ab_pp1a T403I 1.00e+0 AY.133
V6666 5880C>T synonymous_variant ORF1ab_pp1a F1960F 7.06e-1 AY.133
V7511 12558C>T synonymous_variant ORF1ab_pp1a S4186S 7.06e-1 AY.133
V760 2441C>T missense_variant ORF1ab_pp1a T814I 7.05e-1 AY.133
V8295 18492G>A synonymous_variant ORF1ab_pp1ab P6164P 7.06e-1 AY.133
V8274 18342C>T synonymous_variant ORF1ab_pp1ab G6114G 1.00e+0 AY.20.1
V5175 229G>A missense_variant ORF8 G77S 7.49e-1 AY.4.2.4
V3582 205C>T missense_variant S H69Y 1.00e+0 AY.5.2
V5697 35C>T missense_variant ORF10 T12M 1.00e+0 AY.56
V6842 7263C>T synonymous_variant ORF1ab_pp1a V2421V 1.00e+0 AY.56
V6857 7383T>C synonymous_variant ORF1ab_pp1a G2461G 7.04e-1 AZ.2.1
V1576 6737C>T missense_variant ORF1ab_pp1a S2246L 1.00e+0 AZ.5
V482 1328C>T missense_variant ORF1ab_pp1a S443F 1.00e+0 AZ.5
V5401 464C>T missense_variant N A155V 8.16e-1 AZ.5
V3447 20813C>T missense_variant ORF1ab_pp1ab T6938I 8.28e-1 B.1.1.174
V6094 1644C>T synonymous_variant ORF1ab_pp1a F548F 1.00e+0 B.1.1.186
V9076 3438C>T synonymous_variant S D1146D 7.03e-1 B.1.119
V1607 6848C>T missense_variant ORF1ab_pp1a T2283I 1.00e+0 B.1.1.231
V2983 17700G>T missense_variant ORF1ab_pp1ab M5900I 7.06e-1 B.1.1.231
V4084 2434C>T missense_variant S P812S 1.00e+0 B.1.1.231
V7973 16113G>A synonymous_variant ORF1ab_pp1ab P5371P 1.00e+0 B.1.1.231
V4476 310C>T missense_variant ORF3a P104S 1.00e+0 B.1.1.265
V4596 668C>T missense_variant ORF3a T223I 1.00e+0 B.1.1.265
V4814 62C>T missense_variant ORF6 T21I 1.00e+0 B.1.1.265
V4979 296C>T missense_variant ORF7a P99L 1.00e+0 B.1.1.265
V8564 20793C>T synonymous_variant ORF1ab_pp1ab D6931D 1.00e+0 B.1.1.265
V9558 363C>A synonymous_variant ORF8 I121I 1.00e+0 B.1.1.265
V9603 180C>T synonymous_variant N G60G 1.00e+0 B.1.1.265
V9790 1113C>T synonymous_variant N D371D 1.00e+0 B.1.1.265
V1863 8672C>T missense_variant ORF1ab_pp1a A2891V 1.00e+0 B.1.1.351
V106 -14G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.1.354
V6900 7752G>T synonymous_variant ORF1ab_pp1a A2584A 7.06e-1 B.1.1.354
V9213 504C>T synonymous_variant ORF3a V168V 1.00e+0 B.1.1.354
V9496 52C>T synonymous_variant ORF7b L18L 1.00e+0 B.1.1.354
V1646 7217C>T missense_variant ORF1ab_pp1a S2406L -6.27e-1 B.1.1.389
V1790 8307G>T missense_variant ORF1ab_pp1a W2769C 7.70e-1 B.1.1.389
V2021 10058A>G missense_variant ORF1ab_pp1a K3353R -7.70e-1 B.1.1.389
V2026 10075C>T missense_variant ORF1ab_pp1a P3359S 6.62e-1 B.1.1.389
V342 794C>T missense_variant ORF1ab_pp1a T265I -7.70e-1 B.1.1.389
V6221 2451C>T synonymous_variant ORF1ab_pp1a G817G -7.70e-1 B.1.1.389
V7208 10095G>A synonymous_variant ORF1ab_pp1a K3365K 6.62e-1 B.1.1.389
V7254 10452T>C synonymous_variant ORF1ab_pp1a N3484N -7.70e-1 B.1.1.389
V8056 16746C>T synonymous_variant ORF1ab_pp1ab I5582I -7.70e-1 B.1.1.389
V813 2708C>T missense_variant ORF1ab_pp1a A903V -6.62e-1 B.1.1.389
V4866 41C>T missense_variant ORF7a T14I 8.14e-1 B.1.1.413
V7228 10242C>T synonymous_variant ORF1ab_pp1a N3414N 6.61e-1 B.1.1.413
V2153 10994C>T missense_variant ORF1ab_pp1a T3665I 1.00e+0 B.1.1.448
V4310 35C>T missense_variant ORF3a T12I 1.00e+0 B.1.1.448
V1325 5429C>T missense_variant ORF1ab_pp1a P1810L 1.00e+0 B.1.1.452
V5568 951G>T missense_variant N M317I 1.00e+0 B.1.1.452
V6217 2436C>T synonymous_variant ORF1ab_pp1a T812T 1.00e+0 B.1.1.452
V7251 10437C>T synonymous_variant ORF1ab_pp1a D3479D 1.00e+0 B.1.1.452
V9006 2904C>T synonymous_variant S S968S 1.00e+0 B.1.157
V3413 20498C>T missense_variant ORF1ab_pp1ab T6833I 7.06e-1 B.1.160.26
V6454 4278C>T synonymous_variant ORF1ab_pp1a T1426T -7.06e-1 B.1.160.26
V891 3002C>T missense_variant ORF1ab_pp1a T1001I 1.00e+0 B.1.160.26
V7803 14709G>A synonymous_variant ORF1ab_pp1ab K4903K 7.47e-1 B.1.177.53
V4395 154C>T missense_variant ORF3a L52F 1.00e+0 B.1.1.83
V4596 668C>T missense_variant ORF3a T223I 1.00e+0 B.1.1.83
V8107 17139C>T synonymous_variant ORF1ab_pp1ab A5713A 1.00e+0 B.1.1.83
V880 2974G>T missense_variant ORF1ab_pp1a D992Y 1.00e+0 B.1.1.83
V9 -200C>A upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.1.83
V9198 336C>T synonymous_variant ORF3a V112V 1.00e+0 B.1.1.83
V9558 363C>A synonymous_variant ORF8 I121I 1.00e+0 B.1.1.83
V123 70C>T missense_variant ORF1ab_pp1a R24C 7.05e-1 B.1.201
V2556 13907T>C missense_variant ORF1ab_pp1ab I4636T 1.00e+0 B.1.201
V2832 16597G>T missense_variant ORF1ab_pp1ab V5533F 1.00e+0 B.1.201
V3100 18387G>T missense_variant ORF1ab_pp1ab E6129D 1.00e+0 B.1.201
V4596 668C>T missense_variant ORF3a T223I 8.14e-1 B.1.201
V5129 152C>T missense_variant ORF8 A51V 1.00e+0 B.1.201
V6265 2772C>T synonymous_variant ORF1ab_pp1a F924F -7.05e-1 B.1.201
V7108 9375T>C synonymous_variant ORF1ab_pp1a H3125H 1.00e+0 B.1.201
V7504 12516C>T synonymous_variant ORF1ab_pp1a Y4172Y 7.05e-1 B.1.201
V806 2675C>T missense_variant ORF1ab_pp1a P892L -8.14e-1 B.1.201
V8903 2076C>T synonymous_variant S I692I 1.00e+0 B.1.201
V936 3166G>T missense_variant ORF1ab_pp1a V1056L 1.00e+0 B.1.201
V1037 3573G>T missense_variant ORF1ab_pp1a L1191F 7.21e-1 B.1.237
V3748 665C>T missense_variant S A222V 1.00e+0 B.1.237
V4043 2102C>T missense_variant S A701V 1.00e+0 B.1.237
V4542 520G>T missense_variant ORF3a G174C 6.66e-1 B.1.237
V4962 276A>C missense_variant ORF7a E92D 9.15e-1 B.1.237
V5766 *4352G>T downstream_gene_variant S None 9.17e-1 B.1.237
V6538 4879C>T synonymous_variant ORF1ab_pp1a L1627L 1.00e+0 B.1.237
V6922 7881C>T synonymous_variant ORF1ab_pp1a D2627D 1.00e+0 B.1.237
V7742 14319C>T synonymous_variant ORF1ab_pp1ab H4773H 7.73e-1 B.1.237
V8127 17238C>T synonymous_variant ORF1ab_pp1ab F5746F 7.73e-1 B.1.237
V8145 17415G>T synonymous_variant ORF1ab_pp1ab T5805T 9.15e-1 B.1.237
V9347 381T>C synonymous_variant M T127T 9.15e-1 B.1.237
V6479 4449T>C synonymous_variant ORF1ab_pp1a V1483V 1.00e+0 B.1.306
V71 -59C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.306
V7828 14958C>T synonymous_variant ORF1ab_pp1ab F4986F 1.00e+0 B.1.306
V9176 222C>T synonymous_variant ORF3a S74S 1.00e+0 B.1.306
V2672 15013C>T missense_variant ORF1ab_pp1ab H5005Y 7.01e-1 B.1.36.20
V3060 18131C>T missense_variant ORF1ab_pp1ab A6044V 7.01e-1 B.1.36.20
V5559 898C>T missense_variant N H300Y 8.09e-1 B.1.36.20
V6095 1647C>T synonymous_variant ORF1ab_pp1a S549S 8.09e-1 B.1.36.20
V6702 6096C>T synonymous_variant ORF1ab_pp1a D2032D 7.01e-1 B.1.36.20
V6833 7155C>T synonymous_variant ORF1ab_pp1a I2385I 7.01e-1 B.1.36.20
V7403 11697C>T synonymous_variant ORF1ab_pp1a L3899L 1.00e+0 B.1.36.20
V9557 360C>T synonymous_variant ORF8 F120F 7.01e-1 B.1.36.20
V1870 8717C>T missense_variant ORF1ab_pp1a T2906I 1.00e+0 B.1.36.25
V2423 12932C>T missense_variant ORF1ab_pp1a T4311I 1.00e+0 B.1.36.39
V310 619C>T missense_variant ORF1ab_pp1a R207C 9.10e-1 B.1.425
V6002 948C>T synonymous_variant ORF1ab_pp1a C316C 9.75e-1 B.1.425
V7889 15456C>T synonymous_variant ORF1ab_pp1ab D5152D 8.40e-1 B.1.425
V3607 284C>A missense_variant S T95N 1.00e+0 B.1.459
V3741 643G>T missense_variant S D215Y 7.06e-1 B.1.459
V6355 3447A>G synonymous_variant ORF1ab_pp1a L1149L 7.06e-1 B.1.459
V1470 6226A>G missense_variant ORF1ab_pp1a I2076V 1.00e+0 B.1.469
V371 905C>T missense_variant ORF1ab_pp1a S302F 1.00e+0 B.1.469
V4357 109A>G missense_variant ORF3a I37V 1.00e+0 B.1.469
V4600 673G>T missense_variant ORF3a V225F 1.00e+0 B.1.469
V6227 2508C>T synonymous_variant ORF1ab_pp1a Y836Y 1.00e+0 B.1.469
V8799 1296C>T synonymous_variant S C432C 1.00e+0 B.1.469
V940 3199C>T missense_variant ORF1ab_pp1a H1067Y 1.00e+0 B.1.469
V1938 9296C>T missense_variant ORF1ab_pp1a S3099L 8.13e-1 B.1.478
V4229 3505A>T missense_variant S I1169F 8.13e-1 B.1.478
V617 1829C>T missense_variant ORF1ab_pp1a S610L 8.13e-1 B.1.478
V7555 12903C>T synonymous_variant ORF1ab_pp1a H4301H 8.13e-1 B.1.478
V1055 3631G>T missense_variant ORF1ab_pp1a V1211F 1.00e+0 B.1.510
V1071 3683A>G missense_variant ORF1ab_pp1a D1228G 1.00e+0 B.1.510
V1170 4421C>T missense_variant ORF1ab_pp1a T1474I 8.89e-1 B.1.510
V2556 13907T>C missense_variant ORF1ab_pp1ab I4636T 1.00e+0 B.1.510
V3355 20155G>A missense_variant ORF1ab_pp1ab D6719N 1.00e+0 B.1.510
V342 794C>T missense_variant ORF1ab_pp1a T265I -1.00e+0 B.1.510
V4406 171G>T missense_variant ORF3a Q57H -9.00e-1 B.1.510
V4596 668C>T missense_variant ORF3a T223I 1.00e+0 B.1.510
V4935 217C>T missense_variant ORF7a H73Y 7.75e-1 B.1.510
V7897 15510C>T synonymous_variant ORF1ab_pp1ab S5170S 6.55e-1 B.1.510
V2352 12386C>T missense_variant ORF1ab_pp1a T4129I 9.10e-1 B.1.573
V2574 13982A>G missense_variant ORF1ab_pp1ab D4661G 7.06e-1 B.1.575.1
V6157 2073C>T synonymous_variant ORF1ab_pp1a D691D 7.06e-1 B.1.603
V6245 2616C>T synonymous_variant ORF1ab_pp1a A872A 8.21e-1 B.1.603
V7495 12453G>A synonymous_variant ORF1ab_pp1a Q4151Q 8.71e-1 B.1.603
V205 274C>T missense_variant ORF1ab_pp1a L92F 1.00e+0 B.1.605
V2331 12199G>A missense_variant ORF1ab_pp1a A4067T 1.00e+0 B.1.605
V4406 171G>T missense_variant ORF3a Q57H -1.00e+0 B.1.605
V5443 581C>T missense_variant N S194L 1.00e+0 B.1.605
V5467 611G>T missense_variant N G204V 1.00e+0 B.1.605
V616 1826C>T missense_variant ORF1ab_pp1a T609I 1.00e+0 B.1.605
V3030 17949G>T missense_variant ORF1ab_pp1ab M5983I 1.00e+0 B.1.631
V4474 307G>T missense_variant ORF3a A103S 1.00e+0 B.1.631
V8626 60C>T synonymous_variant S T20T 1.00e+0 B.1.631
V91 -34T>C upstream_gene_variant ORF1ab_pp1a None 7.06e-1 B.1.631
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 7.06e-1 B.1.634
V4168 3208G>T missense_variant S A1070S 7.06e-1 B.1.634
V6468 4369T>C synonymous_variant ORF1ab_pp1a L1457L 7.06e-1 B.1.634
V6891 7680C>T synonymous_variant ORF1ab_pp1a Y2560Y 1.00e+0 B.1.634
V7157 9708G>A synonymous_variant ORF1ab_pp1a K3236K 7.06e-1 B.1.634
V4707 -22G>T upstream_gene_variant M None 1.00e+0 B.23
V6630 5547C>T synonymous_variant ORF1ab_pp1a D1849D 1.00e+0 B.23
V74 -56G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.23
V2791 16210A>G missense_variant ORF1ab_pp1ab S5404G 6.29e-1 B.31
V1357 5642C>T missense_variant ORF1ab_pp1a T1881I 1.00e+0 BA.2.10.3
V572 1678C>T missense_variant ORF1ab_pp1a R560C 7.06e-1 BA.2.10.3
V204 269C>T missense_variant ORF1ab_pp1a A90V 1.00e+0 BA.2.17
V7494 12445C>T synonymous_variant ORF1ab_pp1a L4149L 1.00e+0 BA.2.17
V7500 12498C>T synonymous_variant ORF1ab_pp1a D4166D 7.06e-1 BA.2.17
V7919 15678A>G synonymous_variant ORF1ab_pp1ab P5226P 7.06e-1 BA.2.17
V8485 20091A>G synonymous_variant ORF1ab_pp1ab L6697L 1.00e+0 BA.2.17
V7639 13557C>T synonymous_variant ORF1ab_pp1ab L4519L 1.00e+0 BA.2.27
V6938 8016C>T synonymous_variant ORF1ab_pp1a N2672N 1.00e+0 BA.2.9.6
V5576 980C>T missense_variant N S327L 7.06e-1 BA.4.1.10
V6229 2523C>T synonymous_variant ORF1ab_pp1a I841I 1.00e+0 BA.4.1.10
V3939 1640C>A missense_variant S T547K -7.04e-1 BC.2
V2383 12541G>A missense_variant ORF1ab_pp1a V4181I 1.00e+0 BF.19
V2692 15175G>A missense_variant ORF1ab_pp1ab V5059I 1.00e+0 BF.19
V3735 638T>G missense_variant S V213G 7.05e-1 BF.19
V3878 1337G>A missense_variant S G446D 1.00e+0 BF.19
V5122 134G>T missense_variant ORF8 W45L 1.00e+0 BF.19
V8333 18753C>T synonymous_variant ORF1ab_pp1ab F6251F -1.00e+0 BF.19
V8491 20136A>G synonymous_variant ORF1ab_pp1ab E6712E 1.00e+0 BF.19
V2329 12194C>T missense_variant ORF1ab_pp1a T4065I 1.00e+0 BN.1.1.1
V2347 12304G>A missense_variant ORF1ab_pp1a V4102I 6.13e-1 BN.6
V8292 18480C>T synonymous_variant ORF1ab_pp1ab Y6160Y 6.72e-1 BN.6
V867 2920G>A missense_variant ORF1ab_pp1a E974K 1.00e+0 BN.6
V305 601A>G missense_variant ORF1ab_pp1a I201V 1.00e+0 BQ.1.1.21
V6577 5127C>T synonymous_variant ORF1ab_pp1a N1709N 1.00e+0 BQ.1.1.34
V8802 1332G>A synonymous_variant S K444K 1.00e+0 BQ.1.1.34
V8865 1854A>T synonymous_variant S T618T 1.00e+0 BQ.1.1.34
V2860 16775A>G missense_variant ORF1ab_pp1ab N5592S 7.67e-1 BQ.1.20
V6581 5163A>G synonymous_variant ORF1ab_pp1a T1721T 1.00e+0 BQ.1.20
V7341 11262G>A synonymous_variant ORF1ab_pp1a L3754L 1.00e+0 BQ.1.20
V8804 1353C>T synonymous_variant S Y451Y 1.00e+0 BQ.1.20
V9640 420T>C synonymous_variant N N140N 1.00e+0 BQ.1.20
V2015 10031C>T missense_variant ORF1ab_pp1a S3344F 9.41e-1 BQ.1.27
V631 1879G>T missense_variant ORF1ab_pp1a V627F 9.41e-1 BQ.1.27
V6371 3609C>T synonymous_variant ORF1ab_pp1a I1203I 7.96e-1 BQ.1.27
V6480 4455G>A synonymous_variant ORF1ab_pp1a A1485A 9.41e-1 BQ.1.27
V7093 9222C>T synonymous_variant ORF1ab_pp1a Y3074Y 8.78e-1 BQ.1.27
V1211 4652T>C missense_variant ORF1ab_pp1a I1551T 1.00e+0 BQ.1.7
V2178 11080C>T missense_variant ORF1ab_pp1a L3694F 1.00e+0 BQ.1.7
V5286 61T>C missense_variant N S21P 1.00e+0 BQ.1.7
V8650 204A>C synonymous_variant S I68I 7.05e-1 BQ.1.7
V1221 4708G>T missense_variant ORF1ab_pp1a V1570L 1.00e+0 BQ.2
V4501 382T>A missense_variant ORF3a W128R 1.00e+0 BQ.2
V6636 5604C>T synonymous_variant ORF1ab_pp1a Y1868Y 1.00e+0 BQ.2
V8733 765T>C synonymous_variant S S255S 1.00e+0 BQ.2
V9338 351C>T synonymous_variant M N117N 1.00e+0 BQ.2
V5677 -3C>T upstream_gene_variant ORF10 None 1.00e+0 BS.1.1
V7867 15276C>T synonymous_variant ORF1ab_pp1ab V5092V 1.00e+0 BS.1.1
V1755 8022G>T missense_variant ORF1ab_pp1a M2674I 1.00e+0 C.1.2
V5380 401C>T missense_variant N A134V 7.06e-1 C.1.2
V9372 492G>T synonymous_variant M L164L 1.00e+0 C.1.2
V9391 621C>T synonymous_variant M N207N 1.00e+0 C.18
V4604 686C>T missense_variant ORF3a T229I 1.00e+0 C.37.1
V6950 8088G>T synonymous_variant ORF1ab_pp1a A2696A 1.00e+0 C.37.1
V1970 9602T>C missense_variant ORF1ab_pp1a L3201P 1.00e+0 C.38
V342 794C>T missense_variant ORF1ab_pp1a T265I 7.04e-1 C.38
V3550 74C>T missense_variant S P25L 1.00e+0 C.38
V3717 570G>T missense_variant S R190S 1.00e+0 C.38
V3742 644A>G missense_variant S D215G 1.00e+0 C.38
V3755 727_732delGCTTTA conservative_inframe_deletion S A243_L244del 1.00e+0 C.38
V3761 732A>T missense_variant S L244F 1.00e+0 C.38
V4023 2042C>G missense_variant S P681R 1.00e+0 C.38
V4143 2848G>A missense_variant S D950N 1.00e+0 C.38
V4337 77C>T missense_variant ORF3a S26L 1.00e+0 C.38
V4668 61C>A missense_variant E L21I 1.00e+0 C.38
V4689 202T>C missense_variant E S68P 1.00e+0 C.38
V5020 40_41delTT frameshift_variant ORF7b L14fs 1.00e+0 C.38
V5341 188A>G missense_variant N D63G 1.00e+0 C.38
V5617 1132G>C missense_variant N E378Q -1.00e+0 C.38
V5628 1148C>T missense_variant N P383L 1.00e+0 C.38
V5629 1152G>T missense_variant N Q384H 1.00e+0 C.38
V6604 5319A>G synonymous_variant ORF1ab_pp1a T1773T 1.00e+0 C.38
V7538 12754C>T synonymous_variant ORF1ab_pp1a L4252L 1.00e+0 C.38
V8338 18789T>C synonymous_variant ORF1ab_pp1ab I6263I 1.00e+0 C.38
V8671 297C>T synonymous_variant S N99N 1.00e+0 C.38
V8716 648C>T synonymous_variant S L216L 1.00e+0 C.38
V9372 492G>T synonymous_variant M L164L 1.00e+0 C.38
V6029 1176C>T synonymous_variant ORF1ab_pp1a G392G 1.00e+0 C.39
V7394 11667T>C synonymous_variant ORF1ab_pp1a A3889A 6.92e-1 C.39
V9610 234C>T synonymous_variant N S78S 6.92e-1 C.39
V4480 316C>T missense_variant ORF3a L106F 8.64e-1 CH.1.1.4
V5039 94C>T missense_variant ORF7b L32F 8.64e-1 CH.1.1.4
V3173 18854C>T missense_variant ORF1ab_pp1ab A6285V 1.00e+0 CM.10
V6219 2445C>T synonymous_variant ORF1ab_pp1a L815L 1.00e+0 CM.10
V6591 5247C>T synonymous_variant ORF1ab_pp1a N1749N 8.15e-1 CM.10
V7399 11685C>T synonymous_variant ORF1ab_pp1a H3895H 1.00e+0 CM.10
V7019 8652C>T synonymous_variant ORF1ab_pp1a F2884F 7.06e-1 CQ.1
V1414 6047C>T missense_variant ORF1ab_pp1a T2016I 1.00e+0 N.3
V281 496A>G missense_variant ORF1ab_pp1a S166G 1.00e+0 N.3
V2874 16861C>T missense_variant ORF1ab_pp1ab L5621F 1.00e+0 N.3
V3946 1674G>T missense_variant S K558N 1.00e+0 N.3
V4866 41C>T missense_variant ORF7a T14I 1.00e+0 N.3
V7209 10104C>T synonymous_variant ORF1ab_pp1a R3368R 1.00e+0 N.3
V7381 11547C>T synonymous_variant ORF1ab_pp1a G3849G 1.00e+0 N.3
V8222 18003C>T synonymous_variant ORF1ab_pp1ab R6001R 1.00e+0 N.3
V8524 20455C>T synonymous_variant ORF1ab_pp1ab L6819L 1.00e+0 N.3
V8946 2472C>T synonymous_variant S N824N 1.00e+0 N.3
V3121 18562G>T missense_variant ORF1ab_pp1ab V6188F 1.00e+0 P.1.8
V1607 6848C>T missense_variant ORF1ab_pp1a T2283I 1.00e+0 P.4
V5488 634G>A missense_variant N G212S 7.04e-1 P.4
V5676 -4G>T upstream_gene_variant ORF10 None 7.04e-1 P.4
V1821 8468C>T missense_variant ORF1ab_pp1a T2823I 8.42e-1 P.7
V4225 3487G>T missense_variant S D1163Y 7.05e-1 Q.8
V457 1218T>A missense_variant ORF1ab_pp1a F406L 7.05e-1 Q.8
V6501 4632C>T synonymous_variant ORF1ab_pp1a F1544F 7.05e-1 Q.8
V6763 6529C>T synonymous_variant ORF1ab_pp1a L2177L 7.05e-1 Q.8
V9348 385C>T synonymous_variant M L129L 7.05e-1 Q.8
V9400 46C>T synonymous_variant ORF6 L16L 7.05e-1 Q.8
V5272 37C>A missense_variant N P13T 7.06e-1 U.3
V1955 9449C>T missense_variant ORF1ab_pp1a T3150I 1.00e+0 XBB.1.4
V7186 9900C>T synonymous_variant ORF1ab_pp1a Y3300Y 1.00e+0 XBB.1.4
V7282 10704C>T synonymous_variant ORF1ab_pp1a F3568F 1.00e+0 XBC.1.2.1
V1697 7690C>T missense_variant ORF1ab_pp1a L2564F 1.00e+0 Z.1
V6501 4632C>T synonymous_variant ORF1ab_pp1a F1544F 1.00e+0 Z.1





Manual curation of mutation (5619C>T)-related literature from PubMed

The pubmed.mineR and pubmed-mapper were utilized for extracting literature from PubMed, followed by manual filtering.
Note: PubMed: (COVID-19 [Title/Abstract] OR SARS-COV-2 [Title/Abstract]) AND (DNA mutation [Title/Abstract] OR Protein mutation-1 letter [Title/Abstract] OR Protein mutation-3 letter [Title/Abstract]).

DNA level Protein level Paper title Journal name Publication year Pubmed ID