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The current mutation

ID: V2734
DNA: 15642G>T
Protein: Q5214H
Position: 15906








COV2Var annotation categories







Summary information of mutation (15642G>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1ab
  Gene Name   ORF1ab_pp1ab
  Gene Type   protein_coding
  Genome position   15906
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 15642G>T
  Ref Seq: G
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: Q5214H
  Protein 3-letter Mutation: Gln5214His

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 (15642G>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.1.1.159 131 44 3.36e-1
2020-10 B.1.1 131 12 9.16e-2
2020-10 B.1.400 131 12 9.16e-2
2020-11 B.1.1.63 214 35 1.64e-1
2020-11 B.1.1.159 214 32 1.50e-1
2020-11 B.1.1.214 214 20 9.35e-2
2020-12 B.1.1.63 346 85 2.46e-1
2020-12 B.1.2 346 36 1.04e-1
2020-12 B.1.1.214 346 32 9.25e-2
2020-03 B.1 15 5 3.33e-1
2020-03 B.1.1 15 4 2.67e-1
2020-03 B.1.8 15 3 2.00e-1
2020-04 B.1.1 36 22 6.11e-1
2020-04 B.1 36 4 1.11e-1
2020-04 B.1.293 36 3 8.33e-2
2020-05 B.1.1.202 40 24 6.00e-1
2020-05 B.1 40 6 1.50e-1
2020-05 B.1.1 40 4 1.00e-1
2020-06 B.1 34 19 5.59e-1
2020-06 B.1.293 34 10 2.94e-1
2020-06 B.1.1.1 34 1 2.94e-2
2020-07 B.1.293 45 11 2.44e-1
2020-07 B.1 45 5 1.11e-1
2020-07 C.26 45 4 8.89e-2
2020-08 B.1.293 91 16 1.76e-1
2020-08 B.1.426 91 12 1.32e-1
2020-08 B.1 91 11 1.21e-1
2020-09 B.1.1.159 87 28 3.22e-1
2020-09 B.1.210 87 9 1.03e-1
2020-09 B.1.293 87 8 9.20e-2
2021-01 B.1.177.21 432 77 1.78e-1
2021-01 B.1.351 432 36 8.33e-2
2021-01 B.1.1.159 432 34 7.87e-2
2021-10 AY.125 5399 3966 7.35e-1
2021-10 AY.4 5399 232 4.30e-2
2021-10 AY.116 5399 222 4.11e-2
2021-11 AY.125 6402 4495 7.02e-1
2021-11 AY.4 6402 345 5.39e-2
2021-11 AY.116 6402 263 4.11e-2
2021-12 AY.125 4894 3277 6.70e-1
2021-12 AY.4 4894 260 5.31e-2
2021-12 AY.125.1 4894 258 5.27e-2
2021-02 B.1.351 543 235 4.33e-1
2021-02 B.1.177.21 543 44 8.10e-2
2021-02 B.1.1.7 543 32 5.89e-2
2021-03 B.1.351 1166 783 6.72e-1
2021-03 B.1.1.7 1166 88 7.55e-2
2021-03 B.1.427 1166 50 4.29e-2
2021-04 B.1.351 1039 618 5.95e-1
2021-04 B.1.1.7 1039 155 1.49e-1
2021-04 B.1.1.519 1039 113 1.09e-1
2021-05 B.1.351 535 242 4.52e-1
2021-05 B.1.1.7 535 108 2.02e-1
2021-05 B.1.1.519 535 49 9.16e-2
2021-06 B.1.1.7 292 75 2.57e-1
2021-06 AY.125 292 56 1.92e-1
2021-06 B.1.351 292 47 1.61e-1
2021-07 AY.125 4823 4435 9.20e-1
2021-07 B.1.1.7 4823 82 1.70e-2
2021-07 AY.122 4823 41 8.50e-3
2021-08 AY.125 7863 6766 8.60e-1
2021-08 AY.120.2.1 7863 142 1.81e-2
2021-08 AY.116 7863 90 1.14e-2
2021-09 AY.125 5469 4303 7.87e-1
2021-09 AY.116 5469 181 3.31e-2
2021-09 AY.4 5469 152 2.78e-2
2022-01 AY.125 722 337 4.67e-1
2022-01 BA.1.1 722 128 1.77e-1
2022-01 BA.1 722 40 5.54e-2
2022-10 BA.4.6 76 10 1.32e-1
2022-10 BA.5.1.5 76 7 9.21e-2
2022-10 BQ.1 76 7 9.21e-2
2022-11 BQ.1.1 86 11 1.28e-1
2022-11 BA.4.6 86 9 1.05e-1
2022-11 BA.5.2.3 86 9 1.05e-1
2022-12 BQ.1.1 94 19 2.02e-1
2022-12 BQ.1.8 94 12 1.28e-1
2022-12 BA.5.2.3 94 11 1.17e-1
2022-02 BA.1.1 351 168 4.79e-1
2022-02 BA.2 351 58 1.65e-1
2022-02 AY.125 351 20 5.70e-2
2022-03 BA.2 272 115 4.23e-1
2022-03 BA.1.1 272 64 2.35e-1
2022-03 BA.2.9 272 46 1.69e-1
2022-04 BA.2 178 78 4.38e-1
2022-04 BA.2.9 178 64 3.60e-1
2022-04 BA.1.1 178 11 6.18e-2
2022-05 BA.2.9 139 49 3.53e-1
2022-05 BA.2 139 43 3.09e-1
2022-05 BA.4.1 139 18 1.29e-1
2022-06 BA.4.1 108 32 2.96e-1
2022-06 BA.2 108 14 1.30e-1
2022-06 BA.2.42 108 12 1.11e-1
2022-07 BA.4.1 165 31 1.88e-1
2022-07 BA.5.1.23 165 24 1.45e-1
2022-07 BF.5 165 22 1.33e-1
2022-08 BA.5.1.23 136 35 2.57e-1
2022-08 BA.4.1 136 13 9.56e-2
2022-08 BA.5.2.3 136 12 8.82e-2
2022-09 BA.5.2.3 66 8 1.21e-1
2022-09 BA.5.1.21 66 7 1.06e-1
2022-09 BA.4.6 66 6 9.09e-2
2023-01 BQ.1.1 46 5 1.09e-1
2023-01 BQ.1.8 46 4 8.70e-2
2023-01 CH.1.1.3 46 4 8.70e-2
2023-02 CH.1.1 13 4 3.08e-1
2023-02 XBB.1.5 13 4 3.08e-1
2023-02 BF.5 13 1 7.69e-2

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
V2734 AG.1 6.00e-1 9 2020-9-11 2021-2-3
V2734 AY.112.2 1.02e-2 13 2021-1-10 2022-4-12
V2734 AY.116 2.69e-1 847 2021-2-1 2022-1-31
V2734 AY.120 1.47e-2 470 2020-10-26 2022-9-28
V2734 AY.120.2.1 7.89e-2 166 2021-6-6 2022-1-13
V2734 AY.125 9.86e-1 27683 2020-8-11 2022-5-22
V2734 AY.125.1 1.00e+0 157 2021-9-7 2022-1-3
V2734 AY.128 8.99e-1 647 2021-5-3 2022-1-15
V2734 AY.39.1.1 1.50e-2 69 2020-10-27 2022-2-14
V2734 AY.4.2.3 2.14e-2 129 2021-5-28 2022-4-12
V2734 AY.4.6 1.22e-2 163 2020-10-25 2022-3-9
V2734 AY.43.8 1.41e-2 52 2021-1-12 2022-2-15
V2734 AY.61 1.01e-1 189 2021-4-22 2022-1-14
V2734 B.1.1.133 2.73e-2 3 2020-3-22 2021-2-3
V2734 B.1.1.159 4.90e-1 97 2020-8-15 2021-6-26
V2734 B.1.1.161 1.49e-2 3 2020-3-4 2022-12-30
V2734 B.1.1.202 1.00e+0 12 2020-5-10 2020-5-24
V2734 B.1.1.322 4.42e-2 5 2020-4-13 2021-5-12
V2734 B.1.1.332 1.00e-1 4 2020-7-1 2021-3-17
V2734 B.1.1.409 1.81e-2 3 2020-3-18 2022-7-16
V2734 B.1.1.432 6.02e-2 48 2020-4-24 2021-5-8
V2734 B.1.1.522 3.85e-2 2 2021-2-8 2021-4-14
V2734 B.1.1.523 1.18e-2 7 2021-2-2 2022-3-23
V2734 B.1.1.63 8.39e-2 143 2020-6-23 2021-9-22
V2734 B.1.177.21 1.17e-2 145 2020-8-24 2021-5-31
V2734 B.1.177.52 1.82e-2 10 2020-8-18 2021-5-2
V2734 B.1.210 6.02e-2 23 2020-3-10 2021-7-13
V2734 B.1.239 7.30e-2 69 2020-4-9 2021-9-14
V2734 B.1.256 2.54e-2 3 2020-3-22 2021-4-26
V2734 B.1.293 9.00e-1 63 2020-3-16 2021-2-23
V2734 B.1.351 6.32e-2 1977 2020-2-18 2022-10-26
V2734 B.1.36 1.26e-2 91 2020-2-16 2022-7-9
V2734 B.1.397 1.07e-2 2 2020-4-7 2021-9-14
V2734 B.1.400 1.44e-2 37 2020-4-15 2021-8-21
V2734 B.1.408 8.58e-2 23 2020-5-12 2021-4-7
V2734 B.1.426 1.34e-2 16 2020-4-6 2021-4-3
V2734 B.1.562 4.35e-2 2 2020-10-10 2021-3-2
V2734 BA.2.42 1.22e-2 14 2022-3-17 2022-9-18
V2734 BA.4.5 1.78e-2 18 2022-3-25 2022-11-15
V2734 C.26 1.64e-1 23 2020-4-28 2021-8-27






Examining mutation (15642G>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




Association between mutation (15642G>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 -2.53e-1 2.70e-1 -9.38e-1 3.48e-1 Decrease
Deceased -6.30e-2 1.86e-1 -3.39e-1 7.35e-1 Decrease
Homebound 1.05e+0 1.05e+0 9.96e-1 3.19e-1 Increase
Hospitalized 1.16e+0 1.01e-1 1.15e+1 9.35e-31 Increase
Mild -1.48e+0 2.72e-1 -5.43e+0 5.58e-8 Decrease
Recovered -2.76e-1 1.14e-1 -2.42e+0 1.55e-2 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 -1.96e-2 3.73e-2 -5.26e-1 5.99e-1 Decrease
18-39 6.97e-2 2.13e-2 3.28e+0 1.05e-3 Increase
40-64 -1.05e-1 2.16e-2 -4.86e+0 1.18e-6 Decrease
65-84 -1.72e-2 2.97e-2 -5.79e-1 5.62e-1 Decrease
>=85 3.41e-1 5.42e-2 6.29e+0 3.14e-10 Increase

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 -6.28e-2 2.07e-2 -3.03e+0 2.41e-3 Decrease





Investigating natural selection at mutation (15642G>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
RdRp 13468 16236 932 822 361.40 0.00 4.00e-2 B.1.538 FEL

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
RdRp 13468 16236 932 822 1.00e-2 9.70e-1 AY.116 FUBAR
RdRp 13468 16236 932 822 0.00e+0 9.80e-1 AY.128 FUBAR
RdRp 13468 16236 932 822 1.00e-2 9.60e-1 AY.4.2.3 FUBAR
RdRp 13468 16236 932 822 1.00e-2 9.70e-1 B.1.36 FUBAR
RdRp 13468 16236 932 822 1.00e-2 9.60e-1 B.1.400 FUBAR
RdRp 13468 16236 932 822 2.00e-2 9.60e-1 B.1.595 FUBAR
RdRp 13468 16236 932 822 1.00e-2 9.80e-1 B.1.351 FUBAR
RdRp 13468 16236 932 822 1.00e-2 9.70e-1 B.1.621 FUBAR
RdRp 13468 16236 932 822 1.00e-2 9.70e-1 BA.1.1 FUBAR
RdRp 13468 16236 932 822 2.00e-2 9.50e-1 BA.5.2.6 FUBAR
RdRp 13468 16236 932 822 2.00e-2 9.60e-1 AY.117 FUBAR
RdRp 13468 16236 932 822 1.00e-2 9.60e-1 AY.125 FUBAR
RdRp 13468 16236 932 822 1.00e-2 9.80e-1 AY.4 FUBAR
RdRp 13468 16236 932 822 1.00e-2 9.60e-1 B.1.1.159 FUBAR




Alterations in protein physicochemical properties induced by mutation (15642G>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
Mutation ORF1ab_pp1ab 794066.8 6.33 928150 86.87 -0.07
Reference ORF1ab_pp1ab 794057.79 6.32 928150 86.87 -0.07




Alterations in protein stability induced by mutation (15642G>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
Q5214H ORF1ab_pp1ab Point 5214 -1.29 Decrease 7 25 Environment
Q5214H ORF1ab_pp1ab Point 5214 -1.18 Decrease 7.4 37 Internal




Impact on protein function induced by mutation (15642G>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
Q5214H ORF1ab_pp1ab Point 0.083 Altered Cytoplasmic_loop (Pr = 0.27 | P = 6.0e-04)
Altered PPI_hotspot (Pr = 0.23 | P = 0.05)
Gain of Zinc_binding at D5217 (Pr = 0.23 | P = 0.05)
Loss of Phosphorylation at Y5218 (Pr = 0.23 | P = 0.06)
Altered MoRF (Pr = 0.23 | P = 0.10)
Loss of Sulfation at Y5218 (Pr = 0.21 | P = 7.1e-04)
Altered Stability (Pr = 0.18 | P = 0.01)
Gain of Manganese_binding at D5217 (Pr = 0.13 | P = 0.05)
Gain of Copper_binding at Q5214 (Pr = 0.05 | P = 0.03)




Exploring mutation (15642G>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 (15642G>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
Q5214H ORF1ab_pp1ab 15906 Chymotrypsin-low specificity LVKHGDDYVY (pos: 5214)
 NA




Impact of spike protein mutation (15642G>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 (15642G>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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Impact of mutation (15642G>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 (15642G>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
V637 1899G>T missense_variant ORF1ab_pp1a E633D 6.50e-1 AY.25
V2531 13702G>A missense_variant ORF1ab_pp1ab A4568T 6.33e-1 BA.1.1.2
V1813 8399C>T missense_variant ORF1ab_pp1a T2800I 8.07e-1 BA.2.9
V7073 9054C>T synonymous_variant ORF1ab_pp1a F3018F 6.42e-1 B.1.429
V7696 13998C>T synonymous_variant ORF1ab_pp1ab D4666D 7.41e-1 BA.1.15.1
V123 70C>T missense_variant ORF1ab_pp1a R24C 8.66e-1 A.23.1
V2499 13510C>T missense_variant ORF1ab_pp1ab P4504S 1.00e+0 A.23.1
V7273 10605G>T synonymous_variant ORF1ab_pp1a L3535L 7.55e-1 A.23.1
V7344 11298C>T synonymous_variant ORF1ab_pp1a C3766C 1.00e+0 A.23.1
V1013 3463G>T missense_variant ORF1ab_pp1a G1155C 8.65e-1 A.27
V2120 10844C>T missense_variant ORF1ab_pp1a A3615V 7.06e-1 A.27
V7667 13803T>C synonymous_variant ORF1ab_pp1ab N4601N 7.06e-1 A.27
V1240 4787C>T missense_variant ORF1ab_pp1a P1596L 7.07e-1 A.3
V2844 16684C>T missense_variant ORF1ab_pp1ab P5562S 7.07e-1 AD.2
V4183 3259G>T missense_variant S A1087S 8.66e-1 AY.101
V5760 *4350G>A downstream_gene_variant S None 9.61e-1 AY.101
V8470 19971C>T synonymous_variant ORF1ab_pp1ab P6657P 8.19e-1 AY.101
V1451 6163C>T missense_variant ORF1ab_pp1a P2055S 9.23e-1 AY.102
V4414 185T>C missense_variant ORF3a I62T 6.38e-1 AY.106
V6984 8418C>T synonymous_variant ORF1ab_pp1a I2806I 6.32e-1 AY.106
V3715 569G>A missense_variant S R190K 7.07e-1 AY.107
V4259 3672G>T missense_variant S L1224F 7.07e-1 AY.107
V6250 2677C>T synonymous_variant ORF1ab_pp1a L893L 7.07e-1 AY.107
V8010 16383G>A synonymous_variant ORF1ab_pp1ab T5461T 7.07e-1 AY.107
V2561 13922G>T missense_variant ORF1ab_pp1ab R4641M 7.07e-1 AY.108
V8466 19884C>T synonymous_variant ORF1ab_pp1ab F6628F 7.07e-1 AY.108
V3697 542G>T missense_variant S G181V 8.04e-1 AY.109
V4695 217C>T missense_variant E L73F 9.76e-1 AY.109
V6046 1287T>C synonymous_variant ORF1ab_pp1a A429A 9.48e-1 AY.109
V6555 4974C>T synonymous_variant ORF1ab_pp1a Y1658Y 7.06e-1 AY.109
V6657 5775C>T synonymous_variant ORF1ab_pp1a F1925F 9.27e-1 AY.109
V8230 18054G>T synonymous_variant ORF1ab_pp1ab G6018G 6.19e-1 AY.109
V4443 255G>T missense_variant ORF3a L85F 7.70e-1 AY.111
V4546 524C>T missense_variant ORF3a T175I 6.40e-1 AY.111
V51 -83C>T upstream_gene_variant ORF1ab_pp1a None 7.30e-1 AY.111
V2961 17482C>T missense_variant ORF1ab_pp1ab P5828S 8.73e-1 AY.112.2
V4191 3310G>T missense_variant S V1104L 6.18e-1 AY.112.2
V5721 *4295C>T downstream_gene_variant S None 6.18e-1 AY.112.2
V8527 20493T>C synonymous_variant ORF1ab_pp1ab S6831S 8.31e-1 AY.112.2
V2513 13598C>T missense_variant ORF1ab_pp1ab T4533I 8.03e-1 AY.113
V7311 11004T>C synonymous_variant ORF1ab_pp1a D3668D 8.68e-1 AY.113
V1437 6108G>T missense_variant ORF1ab_pp1a M2036I 9.81e-1 AY.114
V7102 9294C>T synonymous_variant ORF1ab_pp1a Y3098Y 6.79e-1 AY.114
V8370 19005C>T synonymous_variant ORF1ab_pp1ab N6335N 6.45e-1 AY.114
V9748 927C>T synonymous_variant N P309P 6.66e-1 AY.114
V1579 6746C>T missense_variant ORF1ab_pp1a A2249V 7.09e-1 AY.116
V4409 175G>A missense_variant ORF3a A59T 7.30e-1 AY.116
V5293 71C>T missense_variant N T24I 9.80e-1 AY.116
V6562 5019C>T synonymous_variant ORF1ab_pp1a N1673N 7.23e-1 AY.116
V7302 10887C>T synonymous_variant ORF1ab_pp1a V3629V 9.81e-1 AY.116
V7414 11760C>T synonymous_variant ORF1ab_pp1a S3920S 9.51e-1 AY.116
V4161 3150G>T missense_variant S M1050I 9.87e-1 AY.120.2.1
V4389 146G>T missense_variant ORF3a G49V 6.79e-1 AY.120.2.1
V4866 41C>T missense_variant ORF7a T14I 7.05e-1 AY.120.2.1
V6939 8025C>T synonymous_variant ORF1ab_pp1a L2675L 9.97e-1 AY.120.2.1
V8359 18922C>T synonymous_variant ORF1ab_pp1ab L6308L 1.00e+0 AY.120.2
V9159 129C>T synonymous_variant ORF3a F43F 7.07e-1 AY.120.2
V8359 18922C>T synonymous_variant ORF1ab_pp1ab L6308L 8.29e-1 AY.120
V1077 3701C>T missense_variant ORF1ab_pp1a A1234V 7.07e-1 AY.124
V2825 16531G>T missense_variant ORF1ab_pp1ab V5511L 9.15e-1 AY.128
V8692 438C>T synonymous_variant S H146H 6.32e-1 AY.15
V9644 432T>C synonymous_variant N D144D 6.70e-1 AY.15
V5594 1075G>T missense_variant N A359S 7.07e-1 AY.16
V8965 2571C>T synonymous_variant S G857G 1.00e+0 AY.1
V1616 6908C>T missense_variant ORF1ab_pp1a S2303F 1.00e+0 AY.23.1
V2026 10075C>T missense_variant ORF1ab_pp1a P3359S 1.00e+0 AY.23.1
V2400 12659C>T missense_variant ORF1ab_pp1a P4220L 1.00e+0 AY.23.1
V3285 19738G>T missense_variant ORF1ab_pp1ab D6580Y 1.00e+0 AY.23.1
V3371 20216C>T missense_variant ORF1ab_pp1ab S6739L 1.00e+0 AY.23.1
V3997 1963C>T missense_variant S H655Y 7.07e-1 AY.23.1
V4428 207G>T missense_variant ORF3a W69C 1.00e+0 AY.23.1
V4953 248C>T missense_variant ORF7a S83L 1.00e+0 AY.23.1
V5049 119C>T missense_variant ORF7b T40I -7.07e-1 AY.23.1
V5747 *4337C>T downstream_gene_variant S None 1.00e+0 AY.23.1
V6770 6618C>T synonymous_variant ORF1ab_pp1a V2206V 1.00e+0 AY.23.1
V9095 3534C>T synonymous_variant S N1178N 1.00e+0 AY.23.1
V9406 93C>T synonymous_variant ORF6 Y31Y 1.00e+0 AY.23.1
V9475 291C>T synonymous_variant ORF7a Y97Y 1.00e+0 AY.23.1
V4351 97G>T missense_variant ORF3a A33S 7.07e-1 AY.24
V9112 3645C>T synonymous_variant S Y1215Y 7.07e-1 AY.24
V3128 18616G>T missense_variant ORF1ab_pp1ab A6206S 8.16e-1 AY.28
V383 945G>T missense_variant ORF1ab_pp1a M315I 8.16e-1 AY.28
V5701 59G>T missense_variant ORF10 R20I 8.16e-1 AY.28
V6109 1761A>G synonymous_variant ORF1ab_pp1a T587T 8.16e-1 AY.28
V6120 1830G>A synonymous_variant ORF1ab_pp1a S610S 8.16e-1 AY.28
V8292 18480C>T synonymous_variant ORF1ab_pp1ab Y6160Y 6.65e-1 AY.28
V347 812C>T missense_variant ORF1ab_pp1a P271L 1.00e+0 AY.2
V8721 663G>T synonymous_variant S S221S 6.32e-1 AY.2
V9357 429G>C synonymous_variant M V143V 8.16e-1 AY.2
V5513 702G>T missense_variant N M234I 6.54e-1 AY.30
V6244 2613C>T synonymous_variant ORF1ab_pp1a F871F 6.54e-1 AY.30
V4658 -15G>T upstream_gene_variant E None 7.07e-1 AY.3.1
V3908 1448T>C missense_variant S V483A 7.97e-1 AY.32
V4640 784C>T missense_variant ORF3a P262S 7.45e-1 AY.32
V1052 3620C>T missense_variant ORF1ab_pp1a P1207L 8.16e-1 AY.37
V1201 4625C>T missense_variant ORF1ab_pp1a T1542I 1.00e+0 AY.37
V1607 6848C>T missense_variant ORF1ab_pp1a T2283I 1.00e+0 AY.37
V4932 211G>T missense_variant ORF7a V71L 1.00e+0 AY.37
V6451 4245G>T synonymous_variant ORF1ab_pp1a V1415V 8.16e-1 AY.37
V6892 7683C>T synonymous_variant ORF1ab_pp1a Y2561Y 1.00e+0 AY.37
V7787 14613C>T synonymous_variant ORF1ab_pp1ab Y4871Y 1.00e+0 AY.37
V8915 2196C>T synonymous_variant S T732T 8.16e-1 AY.37
V9796 1149G>A synonymous_variant N P383P 1.00e+0 AY.37
V3514 21274G>T missense_variant ORF1ab_pp1ab V7092F 9.57e-1 AY.39.1.4
V8124 17214G>A synonymous_variant ORF1ab_pp1ab K5738K 9.39e-1 AY.39.1.4
V8522 20439C>T synonymous_variant ORF1ab_pp1ab Y6813Y 8.26e-1 AY.39.1.4
V122 46C>T missense_variant ORF1ab_pp1a L16F 7.07e-1 AY.39.2
V1709 7775A>G missense_variant ORF1ab_pp1a D2592G 1.00e+0 AY.39.2
V8376 19104A>G synonymous_variant ORF1ab_pp1ab P6368P 1.00e+0 AY.39.2
V981 3337C>T missense_variant ORF1ab_pp1a H1113Y 1.00e+0 AY.39.2
V3559 86C>T missense_variant S T29I 6.37e-1 AY.4.11
V9645 435C>T synonymous_variant N H145H 6.27e-1 AY.4.11
V5038 92C>T missense_variant ORF7b S31L 1.00e+0 AY.41
V7511 12558C>T synonymous_variant ORF1ab_pp1a S4186S 1.00e+0 AY.41
V3371 20216C>T missense_variant ORF1ab_pp1ab S6739L 6.55e-1 AY.4.2.3
V6952 8103G>T synonymous_variant ORF1ab_pp1a A2701A 8.14e-1 AY.4.2.3
V9060 3342C>T synonymous_variant S I1114I 8.65e-1 AY.43.1
V1516 6383C>T missense_variant ORF1ab_pp1a A2128V 9.07e-1 AY.43.8
V3002 17822C>T missense_variant ORF1ab_pp1ab T5941I 9.50e-1 AY.43.8
V379 926C>T missense_variant ORF1ab_pp1a P309L 6.48e-1 AY.43.8
V454 1208C>T missense_variant ORF1ab_pp1a T403I 1.00e+0 AY.46.1
V4854 22G>A missense_variant ORF7a A8T 1.00e+0 AY.46.1
V3347 20133G>T missense_variant ORF1ab_pp1ab K6711N 1.00e+0 AY.46.2
V567 1661C>T missense_variant ORF1ab_pp1a T554I 1.00e+0 AY.46.2
V5738 *4324C>T downstream_gene_variant S None 7.07e-1 AY.46.2
V8843 1686C>T synonymous_variant S F562F 1.00e+0 AY.46.2
V5198 308C>T missense_variant ORF8 S103L 7.45e-1 AY.4.6
V5578 1001C>T missense_variant N T334I 7.25e-1 AY.4.6
V5677 -3C>T upstream_gene_variant ORF10 None 7.41e-1 AY.4.6
V8742 852C>T synonymous_variant S T284T 7.37e-1 AY.4.6
V1150 4282A>G missense_variant ORF1ab_pp1a K1428E 6.67e-1 AY.46
V242 370C>T missense_variant ORF1ab_pp1a R124C 7.07e-1 AY.51
V3400 20445G>T missense_variant ORF1ab_pp1ab M6815I 7.07e-1 AY.51
V4918 184C>T stop_gained ORF7a Q62* 7.07e-1 AY.51
V6858 7401T>C synonymous_variant ORF1ab_pp1a D2467D 7.07e-1 AY.51
V7222 10191C>T synonymous_variant ORF1ab_pp1a F3397F 7.07e-1 AY.51
V9818 1257C>T synonymous_variant N A419A 7.07e-1 AY.51
V2865 16794G>T missense_variant ORF1ab_pp1ab M5598I 1.00e+0 AY.53
V123 70C>T missense_variant ORF1ab_pp1a R24C 1.00e+0 AY.5.4
V1179 4513A>G missense_variant ORF1ab_pp1a I1505V 7.07e-1 AY.59
V6197 2328T>C synonymous_variant ORF1ab_pp1a A776A 1.00e+0 AY.59
V2444 13160G>A missense_variant ORF1ab_pp1a R4387H 7.53e-1 AY.61
V3603 253C>T missense_variant S P85S 6.35e-1 AY.61
V9267 69C>T synonymous_variant E F23F 6.26e-1 AY.61
V1052 3620C>T missense_variant ORF1ab_pp1a P1207L 1.00e+0 AY.67
V1607 6848C>T missense_variant ORF1ab_pp1a T2283I 1.00e+0 AY.67
V260 421_429delAAGTCATTT conservative_inframe_deletion ORF1ab_pp1a K141_F143del 7.24e-1 AY.67
V4273 3711G>T missense_variant S M1237I 9.12e-1 AY.67
V6451 4245G>T synonymous_variant ORF1ab_pp1a V1415V 1.00e+0 AY.67
V6553 4956C>T synonymous_variant ORF1ab_pp1a H1652H 7.74e-1 AY.67
V7787 14613C>T synonymous_variant ORF1ab_pp1ab Y4871Y 1.00e+0 AY.67
V8915 2196C>T synonymous_variant S T732T 1.00e+0 AY.67
V9796 1149G>A synonymous_variant N P383P 1.00e+0 AY.67
V4123 2766G>T missense_variant S L922F 9.04e-1 AY.68
V4273 3711G>T missense_variant S M1237I 8.18e-1 AY.68
V6095 1647C>T synonymous_variant ORF1ab_pp1a S549S 9.04e-1 AY.68
V6460 4314T>A synonymous_variant ORF1ab_pp1a L1438L 9.26e-1 AY.70
V3563 145C>T missense_variant S H49Y 7.07e-1 AY.7.2
V1607 6848C>T missense_variant ORF1ab_pp1a T2283I 7.07e-1 AY.73
V2809 16430C>T missense_variant ORF1ab_pp1ab T5477I 7.07e-1 AY.73
V4589 657G>T missense_variant ORF3a L219F 7.07e-1 AY.73
V4991 332C>T missense_variant ORF7a T111I 7.07e-1 AY.73
V6170 2151C>T synonymous_variant ORF1ab_pp1a Y717Y 7.07e-1 AY.73
V6179 2197C>T synonymous_variant ORF1ab_pp1a L733L 7.07e-1 AY.73
V8915 2196C>T synonymous_variant S T732T 7.07e-1 AY.73
V3327 20011G>T missense_variant ORF1ab_pp1ab D6671Y 8.30e-1 AY.75
V6861 7423C>T synonymous_variant ORF1ab_pp1a L2475L 8.91e-1 AY.75
V1567 6629G>T missense_variant ORF1ab_pp1a C2210F 7.07e-1 AY.77
V1592 6782C>T missense_variant ORF1ab_pp1a S2261F 7.07e-1 AY.77
V1937 9269C>T missense_variant ORF1ab_pp1a T3090I 7.07e-1 AY.77
V418 1082C>T missense_variant ORF1ab_pp1a P361L 7.07e-1 AY.77
V5639 1193C>T missense_variant N A398V 7.07e-1 AY.77
V822 2776C>T missense_variant ORF1ab_pp1a P926S 7.07e-1 AY.77
V8767 1065G>A synonymous_variant S R355R 7.07e-1 AY.77
V6701 6093G>A synonymous_variant ORF1ab_pp1a E2031E 7.94e-1 AY.85
V8588 20970C>T synonymous_variant ORF1ab_pp1ab A6990A 1.00e+0 AY.86
V1903 8981C>T missense_variant ORF1ab_pp1a A2994V 1.00e+0 AY.88
V2975 17558C>T missense_variant ORF1ab_pp1ab P5853L 1.00e+0 AY.88
V7517 12600T>C synonymous_variant ORF1ab_pp1a D4200D 6.54e-1 AY.88
V8985 2775C>T synonymous_variant S N925N 1.00e+0 AY.88
V1004 3427G>T missense_variant ORF1ab_pp1a V1143F 9.26e-1 AY.92
V4065 2294G>T missense_variant S R765L 9.26e-1 AY.92
V5595 1085C>A missense_variant N T362K 8.57e-1 AY.92
V8982 2757C>T synonymous_variant S N919N 9.26e-1 AY.92
V9213 504C>T synonymous_variant ORF3a V168V 7.07e-1 AY.98.1
V4959 266G>T missense_variant ORF7a R89I 7.07e-1 AY.99
V6461 4317C>T synonymous_variant ORF1ab_pp1a N1439N 7.07e-1 AY.99
V7311 11004T>C synonymous_variant ORF1ab_pp1a D3668D 7.07e-1 AY.99
V115 13G>A missense_variant ORF1ab_pp1a V5I 6.68e-1 AY.9
V7353 11388C>T synonymous_variant ORF1ab_pp1a L3796L 1.00e+0 AZ.2
V805 2674C>T missense_variant ORF1ab_pp1a P892S 7.07e-1 B.1.110.3
V1211 4652T>C missense_variant ORF1ab_pp1a I1551T 1.00e+0 B.1.1.198
V135 89G>C missense_variant ORF1ab_pp1a G30A 1.00e+0 B.1.1.198
V143 119C>T missense_variant ORF1ab_pp1a S40L 1.00e+0 B.1.1.198
V1559 6590C>T missense_variant ORF1ab_pp1a T2197I 1.00e+0 B.1.1.198
V1561 6600G>T missense_variant ORF1ab_pp1a K2200N 1.00e+0 B.1.1.198
V1885 8855C>T missense_variant ORF1ab_pp1a T2952I 1.00e+0 B.1.1.198
V1897 8939A>C missense_variant ORF1ab_pp1a D2980A 1.00e+0 B.1.1.198
V2639 14610G>T missense_variant ORF1ab_pp1ab K4870N 1.00e+0 B.1.1.198
V3158 18754C>T missense_variant ORF1ab_pp1ab P6252S 1.00e+0 B.1.1.198
V4182 3253G>A missense_variant S G1085R 1.00e+0 B.1.1.198
V5255 17C>T missense_variant N P6L 1.00e+0 B.1.1.198
V5653 1240G>T missense_variant N A414S 1.00e+0 B.1.1.198
V5694 28C>T missense_variant ORF10 P10S 1.00e+0 B.1.1.198
V7345 11307C>T synonymous_variant ORF1ab_pp1a F3769F 1.00e+0 B.1.1.198
V7416 11778C>T synonymous_variant ORF1ab_pp1a D3926D 1.00e+0 B.1.1.198
V7829 14973C>T synonymous_variant ORF1ab_pp1ab H4991H 1.00e+0 B.1.1.198
V864 2912C>T missense_variant ORF1ab_pp1a P971L 1.00e+0 B.1.1.198
V9151 102G>T synonymous_variant ORF3a T34T 1.00e+0 B.1.1.198
V9278 192T>C synonymous_variant E N64N 1.00e+0 B.1.1.198
V9379 543G>A synonymous_variant M L181L 1.00e+0 B.1.1.198
V3525 26C>T missense_variant S P9L 6.12e-1 B.1.1.1
V7027 8721C>T synonymous_variant ORF1ab_pp1a D2907D 7.07e-1 B.1.1.1
V1010 3452C>T missense_variant ORF1ab_pp1a A1151V 7.07e-1 B.1.1.216
V2098 10731G>T missense_variant ORF1ab_pp1a K3577N 7.07e-1 B.1.1.216
V2353 12398C>T missense_variant ORF1ab_pp1a A4133V 7.07e-1 B.1.1.216
V2485 13448A>G missense_variant ORF1ab_pp1ab K4483R 7.07e-1 B.1.1.216
V3327 20011G>T missense_variant ORF1ab_pp1ab D6671Y 7.07e-1 B.1.1.216
V3665 458T>C missense_variant S M153T 7.07e-1 B.1.1.216
V4009 2024A>G missense_variant S Q675R 7.07e-1 B.1.1.216
V4215 3430G>C missense_variant S E1144Q 7.07e-1 B.1.1.216
V5243 -2A>T upstream_gene_variant N None 7.07e-1 B.1.1.216
V6806 6900C>T synonymous_variant ORF1ab_pp1a T2300T 7.07e-1 B.1.1.216
V7678 13857A>G synonymous_variant ORF1ab_pp1ab P4619P 7.07e-1 B.1.1.216
V7846 15108G>T synonymous_variant ORF1ab_pp1ab T5036T 7.07e-1 B.1.1.216
V8226 18042C>T synonymous_variant ORF1ab_pp1ab F6014F 7.07e-1 B.1.1.216
V8545 20664T>C synonymous_variant ORF1ab_pp1ab P6888P 7.07e-1 B.1.1.216
V8810 1425C>A synonymous_variant S A475A 7.07e-1 B.1.1.216
V1907 9079C>T missense_variant ORF1ab_pp1a L3027F 8.70e-1 B.1.1.222
V3027 17922G>T missense_variant ORF1ab_pp1ab M5974I 7.30e-1 B.1.1.222
V7578 13032C>T synonymous_variant ORF1ab_pp1a D4344D 8.52e-1 B.1.1.222
V882 2977G>T missense_variant ORF1ab_pp1a G993C 8.52e-1 B.1.1.222
V956 3245C>T missense_variant ORF1ab_pp1a A1082V 9.29e-1 B.1.1.222
V1687 7604C>T missense_variant ORF1ab_pp1a S2535L 7.54e-1 B.1.1.232
V181 245_259delGTCATGTTATGGTTG disruptive_inframe_deletion ORF1ab_pp1a G82_V86del 8.65e-1 B.1.1.232
V5559 898C>T missense_variant N H300Y 1.00e+0 B.1.1.263
V1582 6762G>T missense_variant ORF1ab_pp1a M2254I 1.00e+0 B.1.1.279
V3539 62G>C missense_variant S R21T 1.00e+0 B.1.1.28
V3584 208G>T missense_variant S V70F 7.07e-1 B.1.1.28
V5153 194C>T missense_variant ORF8 A65V 7.07e-1 B.1.1.294
V5325 109T>C missense_variant N S37P 1.00e+0 B.1.1.294
V5734 *4321G>T downstream_gene_variant S None 1.00e+0 B.1.1.294
V5794 *4371G>T downstream_gene_variant S None 1.00e+0 B.1.1.294
V7057 8925G>T synonymous_variant ORF1ab_pp1a V2975V 1.00e+0 B.1.1.294
V7711 14098C>T synonymous_variant ORF1ab_pp1ab L4700L 1.00e+0 B.1.1.294
V9495 51G>T synonymous_variant ORF7b L17L 1.00e+0 B.1.1.294
V5085 46T>C missense_variant ORF8 F16L 7.07e-1 B.1.1.33
V5667 -13C>A upstream_gene_variant ORF10 None 7.07e-1 B.1.1.33
V9286 12C>T synonymous_variant M S4S 7.07e-1 B.1.1.33
V3100 18387G>T missense_variant ORF1ab_pp1ab E6129D 9.78e-1 B.1.1.432
V3360 20169G>T missense_variant ORF1ab_pp1ab M6723I 9.43e-1 B.1.1.432
V4382 134G>T missense_variant ORF3a W45L 9.89e-1 B.1.1.432
V4975 289T>C missense_variant ORF7a Y97H 8.34e-1 B.1.1.432
V5222 357_358insCTG conservative_inframe_insertion ORF8 D119_F120insL 6.96e-1 B.1.1.432
V5228 361delA frameshift_variant ORF8 I121fs 6.81e-1 B.1.1.432
V8036 16623C>T synonymous_variant ORF1ab_pp1ab Y5541Y 7.71e-1 B.1.1.432
V8546 20667G>A synonymous_variant ORF1ab_pp1ab T6889T 8.34e-1 B.1.1.432
V3598 238G>T missense_variant S D80Y 7.12e-1 B.1.1.519
V507 1416G>T missense_variant ORF1ab_pp1a E472D 9.16e-1 B.1.1.519
V5578 1001C>T missense_variant N T334I 1.00e+0 B.1.1.523
V9037 3195G>T synonymous_variant S V1065V 1.00e+0 B.1.1.523
V4681 151C>T missense_variant E L51F 9.04e-1 B.1.160.16
V9323 279C>T synonymous_variant M L93L 8.65e-1 B.1.160.16
V1136 4145C>T missense_variant ORF1ab_pp1a A1382V 8.51e-1 B.1.1.63
V1665 7484C>T missense_variant ORF1ab_pp1a T2495I 1.00e+0 B.1.1.63
V3657 443A>C missense_variant S N148T 9.96e-1 B.1.1.63
V4669 61C>T missense_variant E L21F 8.37e-1 B.1.1.63
V6356 3471C>T synonymous_variant ORF1ab_pp1a D1157D 8.70e-1 B.1.1.63
V6833 7155C>T synonymous_variant ORF1ab_pp1a I2385I 9.85e-1 B.1.1.63
V7540 12780G>A synonymous_variant ORF1ab_pp1a V4260V 1.00e+0 B.1.1.63
V8637 135C>A synonymous_variant S S45S 8.38e-1 B.1.1.63
V1780 8215C>T missense_variant ORF1ab_pp1a P2739S 1.00e+0 B.1.177.18
V619 1841C>T missense_variant ORF1ab_pp1a T614I 9.30e-1 B.1.177.21
V8298 18531C>T synonymous_variant ORF1ab_pp1ab N6177N 7.07e-1 B.1.177.4
V1825 8495C>T missense_variant ORF1ab_pp1a A2832V 1.00e+0 B.1.177.52
V1981 9763A>G missense_variant ORF1ab_pp1a T3255A 1.00e+0 B.1.177.52
V2116 10818G>T missense_variant ORF1ab_pp1a L3606F 8.42e-1 B.1.177.52
V3520 13C>T missense_variant S L5F 8.42e-1 B.1.177.52
V3797 790G>T missense_variant S A264S 1.00e+0 B.1.177.52
V5038 92C>T missense_variant ORF7b S31L 9.53e-1 B.1.177.52
V5882 252T>C synonymous_variant ORF1ab_pp1a V84V 1.00e+0 B.1.177.52
V7043 8865G>T synonymous_variant ORF1ab_pp1a V2955V 1.00e+0 B.1.177.52
V7376 11517A>G synonymous_variant ORF1ab_pp1a K3839K 1.00e+0 B.1.177.52
V980 3328C>T missense_variant ORF1ab_pp1a L1110F 9.53e-1 B.1.177.52
V9151 102G>T synonymous_variant ORF3a T34T 8.66e-1 B.1.177.60
V8755 960C>T synonymous_variant S V320V 8.66e-1 B.1.177.82
V5456 602G>T missense_variant N S201I 7.07e-1 B.1.214.2
V8011 16383G>T synonymous_variant ORF1ab_pp1ab T5461T 1.00e+0 B.1.214.2
V1195 4595A>G missense_variant ORF1ab_pp1a D1532G 8.73e-1 B.1.221
V1110 3893C>T missense_variant ORF1ab_pp1a A1298V 7.54e-1 B.1.239
V6043 1263C>T synonymous_variant ORF1ab_pp1a A421A 9.03e-1 B.1.239
V6395 3819C>T synonymous_variant ORF1ab_pp1a D1273D 9.61e-1 B.1.239
V8017 16437T>C synonymous_variant ORF1ab_pp1ab R5479R 9.53e-1 B.1.239
V8325 18684G>T synonymous_variant ORF1ab_pp1ab L6228L 9.85e-1 B.1.239
V8391 19224C>T synonymous_variant ORF1ab_pp1ab V6408V 8.86e-1 B.1.239
V4677 122C>T missense_variant E A41V 1.00e+0 B.1.240
V6451 4245G>T synonymous_variant ORF1ab_pp1a V1415V 8.16e-1 B.1.241
V5981 825T>C synonymous_variant ORF1ab_pp1a F275F 7.07e-1 B.1.258
V6577 5127C>T synonymous_variant ORF1ab_pp1a N1709N 9.48e-1 B.1.349
V2212 11257T>G missense_variant ORF1ab_pp1a F3753V 6.12e-1 B.1.351.2
V7065 8976A>G synonymous_variant ORF1ab_pp1a S2992S 9.69e-1 B.1.351
V9303 123C>T synonymous_variant M N41N 6.86e-1 B.1.351
V384 953C>T missense_variant ORF1ab_pp1a S318L 7.07e-1 B.1.36.22
V5879 243T>C synonymous_variant ORF1ab_pp1a H81H 1.00e+0 B.1.36.22
V6187 2244C>T synonymous_variant ORF1ab_pp1a P748P 7.07e-1 B.1.36.22
V6630 5547C>T synonymous_variant ORF1ab_pp1a D1849D 1.00e+0 B.1.36.22
V6804 6897C>T synonymous_variant ORF1ab_pp1a D2299D 7.07e-1 B.1.36.22
V7464 12135C>T synonymous_variant ORF1ab_pp1a L4045L 7.07e-1 B.1.36.22
V7967 16065C>T synonymous_variant ORF1ab_pp1ab Y5355Y 1.00e+0 B.1.36.22
V8431 19590C>T synonymous_variant ORF1ab_pp1ab D6530D 1.00e+0 B.1.36.22
V9777 1038C>T synonymous_variant N F346F 1.00e+0 B.1.36.22
V2156 11007G>T missense_variant ORF1ab_pp1a M3669I 1.00e+0 B.1.36.8
V4273 3711G>T missense_variant S M1237I 7.07e-1 B.1.36.8
V4695 217C>T missense_variant E L73F 1.00e+0 B.1.36.8
V6310 3153G>A synonymous_variant ORF1ab_pp1a K1051K 1.00e+0 B.1.36.8
V7269 10569C>T synonymous_variant ORF1ab_pp1a A3523A 1.00e+0 B.1.36.8
V8569 20859G>T synonymous_variant ORF1ab_pp1ab G6953G 1.00e+0 B.1.36.8
V8431 19590C>T synonymous_variant ORF1ab_pp1ab D6530D 7.32e-1 B.1.36
V7508 12552G>A synonymous_variant ORF1ab_pp1a L4184L 6.89e-1 B.1.400
V4406 171G>T missense_variant ORF3a Q57H -6.15e-1 B.1.426
V1441 6136C>T missense_variant ORF1ab_pp1a P2046S 6.81e-1 B.1.438.1
V6204 2379C>A synonymous_variant ORF1ab_pp1a I793I 7.21e-1 B.1.438.1
V9765 987G>A synonymous_variant N T329T 7.04e-1 B.1.438.1
V2048 10361C>T missense_variant ORF1ab_pp1a A3454V 7.13e-1 B.1.509
V2212 11257T>G missense_variant ORF1ab_pp1a F3753V 7.07e-1 B.1.517
V5485 631G>A missense_variant N A211T 1.00e+0 B.1.517
V9326 304C>T synonymous_variant M L102L 7.07e-1 B.1.525
V6602 5310C>T synonymous_variant ORF1ab_pp1a Y1770Y 7.95e-1 B.1.526
V6923 7887C>T synonymous_variant ORF1ab_pp1a V2629V 1.00e+0 B.1.560
V7043 8865G>T synonymous_variant ORF1ab_pp1a V2955V 7.07e-1 B.1.560
V8358 18921C>T synonymous_variant ORF1ab_pp1ab C6307C 1.00e+0 B.1.560
V2187 11152G>A missense_variant ORF1ab_pp1a V3718I 1.00e+0 B.1.561
V2371 12491C>T missense_variant ORF1ab_pp1a T4164I 1.00e+0 B.1.561
V5880 246T>C synonymous_variant ORF1ab_pp1a G82G 7.07e-1 B.1.561
V1263 4919C>T missense_variant ORF1ab_pp1a P1640L 6.38e-1 B.1.595
V2189 11153T>C missense_variant ORF1ab_pp1a V3718A 6.38e-1 B.1.595
V2325 12145A>G missense_variant ORF1ab_pp1a I4049V 6.82e-1 B.1.595
V4048 2147C>T missense_variant S T716I 6.38e-1 B.1.595
V4609 718C>T missense_variant ORF3a P240S 6.82e-1 B.1.595
V6928 7914G>A synonymous_variant ORF1ab_pp1a R2638R 8.39e-1 B.1.595
V7914 15660C>T synonymous_variant ORF1ab_pp1ab Y5220Y 8.97e-1 B.1.595
V8154 17469C>T synonymous_variant ORF1ab_pp1ab F5823F 6.38e-1 B.1.595
V3149 18721G>T missense_variant ORF1ab_pp1ab V6241F 6.83e-1 B.1.617.1
V4430 214G>T missense_variant ORF3a A72S 6.36e-1 B.1.617.1
V5055 127G>A missense_variant ORF7b A43T 7.97e-1 B.1.617.1
V1462 6206C>T missense_variant ORF1ab_pp1a T2069I 7.07e-1 B.1.621.2
V9455 210C>T synonymous_variant ORF7a G70G 7.07e-1 B.1.621.2
V5074 23G>A missense_variant ORF8 G8E 1.00e+0 BA.1.1.13
V7636 13497C>T synonymous_variant ORF1ab_pp1ab D4499D 1.00e+0 BA.1.13
V3782 764C>T missense_variant S S255F 1.00e+0 BA.1.14.2
V1499 6308C>T missense_variant ORF1ab_pp1a S2103F 1.00e+0 BA.1.15.2
V1144 4202C>T missense_variant ORF1ab_pp1a T1401I 7.07e-1 BA.1.19
V9606 198C>T synonymous_variant N F66F 7.07e-1 BA.1.19
V2967 17498C>T missense_variant ORF1ab_pp1ab A5833V 1.00e+0 BA.2.10.2
V4314 44T>C missense_variant ORF3a L15S 1.00e+0 BA.2.10.2
V4716 4G>T missense_variant M A2S 7.07e-1 BA.2.13
V1422 6071C>T missense_variant ORF1ab_pp1a S2024L 8.16e-1 BA.2.3.13
V1626 7034C>T missense_variant ORF1ab_pp1a A2345V 8.66e-1 BA.2.3.13
V7319 11079C>T synonymous_variant ORF1ab_pp1a I3693I 1.00e+0 BA.2.3.13
V3492 21100C>T missense_variant ORF1ab_pp1ab P7034S 1.00e+0 BA.2.3.14
V6847 7308C>T synonymous_variant ORF1ab_pp1a V2436V 1.00e+0 BA.2.3.14
V1415 6052C>T missense_variant ORF1ab_pp1a P2018S 1.00e+0 BA.2.3.20
V3209 19126C>T missense_variant ORF1ab_pp1ab P6376S 1.00e+0 BA.2.3.20
V6710 6129T>C synonymous_variant ORF1ab_pp1a D2043D 1.00e+0 BA.2.3.20
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 9.63e-1 BA.2.42
V3484 21040C>A missense_variant ORF1ab_pp1ab R7014S 7.77e-1 BA.2.42
V4777 407G>A missense_variant M S136N 8.96e-1 BA.2.42
V6231 2538T>C synonymous_variant ORF1ab_pp1a D846D 1.00e+0 BA.2.42
V7376 11517A>G synonymous_variant ORF1ab_pp1a K3839K 9.28e-1 BA.2.42
V8449 19719C>T synonymous_variant ORF1ab_pp1ab V6573V 7.54e-1 BA.2.42
V2400 12659C>T missense_variant ORF1ab_pp1a P4220L 1.00e+0 BA.2.75.2
V3062 18137C>T missense_variant ORF1ab_pp1ab P6046L 1.00e+0 BA.2.75.2
V9812 1242T>C synonymous_variant N A414A 7.07e-1 BA.2.75.2
V4544 521G>A missense_variant ORF3a G174D 8.45e-1 BA.2.76
V4994 346C>T missense_variant ORF7a L116F 7.07e-1 BA.2.9.5
V9765 987G>A synonymous_variant N T329T 1.00e+0 BA.2.9.5
V4721 11C>T missense_variant M S4F 1.00e+0 BA.4.2
V5703 64A>G missense_variant ORF10 N22D 7.07e-1 BA.4.2
V9657 475C>T synonymous_variant N L159L 7.07e-1 BA.4.2
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 8.14e-1 BA.4.5
V1313 5354T>C missense_variant ORF1ab_pp1a I1785T 8.80e-1 BA.4.5
V2129 10874C>T missense_variant ORF1ab_pp1a A3625V 8.48e-1 BA.4.5
V9250 768T>C synonymous_variant ORF3a V256V 8.14e-1 BA.4.5
V4429 214G>A missense_variant ORF3a A72T 7.07e-1 BA.4.6.1
V5815 *4397G>T downstream_gene_variant S None 7.07e-1 BA.4.6.1
V7052 8901C>T synonymous_variant ORF1ab_pp1a T2967T 1.00e+0 BA.4.6.1
V3461 20893G>A missense_variant ORF1ab_pp1ab V6965M 1.00e+0 BA.5.1.15
V4590 659G>T missense_variant ORF3a S220I 1.00e+0 BA.5.1.15
V8056 16746C>T synonymous_variant ORF1ab_pp1ab I5582I 1.00e+0 BA.5.1.15
V3665 458T>C missense_variant S M153T 1.00e+0 BA.5.1.21
V4903 139C>T missense_variant ORF7a H47Y 1.00e+0 BA.5.1.21
V8746 882C>T synonymous_variant S D294D 8.81e-1 BA.5.1.21
V2521 13657G>T missense_variant ORF1ab_pp1ab D4553Y 7.55e-1 BA.5.1.23
V5382 404C>T missense_variant N T135I 7.25e-1 BA.5.1.23
V9176 222C>T synonymous_variant ORF3a S74S 9.12e-1 BA.5.1.23
V5397 452C>T missense_variant N P151L 1.00e+0 BA.5.1.24
V656 1981G>A missense_variant ORF1ab_pp1a G661S 9.35e-1 BA.5.1.30
V7417 11784C>T synonymous_variant ORF1ab_pp1a N3928N 8.16e-1 BA.5.1.30
V9095 3534C>T synonymous_variant S N1178N 6.86e-1 BA.5.1.30
V9619 294C>T synonymous_variant N D98D 1.00e+0 BA.5.1.6
V314 635C>T missense_variant ORF1ab_pp1a S212L 7.01e-1 BA.5.2.20
V8107 17139C>T synonymous_variant ORF1ab_pp1ab A5713A 7.07e-1 BA.5.2.21
V8609 21144T>C synonymous_variant ORF1ab_pp1ab F7048F 1.00e+0 BA.5.2.21
V6189 2253G>T synonymous_variant ORF1ab_pp1a V751V 1.00e+0 BA.5.2.24
V3447 20813C>T missense_variant ORF1ab_pp1ab T6938I 8.16e-1 BA.5.2.28
V4040 2081C>T missense_variant S A694V 8.16e-1 BA.5.2.28
V6293 2991T>C synonymous_variant ORF1ab_pp1a N997N 7.07e-1 BA.5.2.6
V502 1387A>G missense_variant ORF1ab_pp1a I463V 6.32e-1 BA.5.2.9
V8681 363T>C synonymous_variant S N121N 1.00e+0 BA.5.2.9
V9511 51C>T synonymous_variant ORF8 H17H 7.07e-1 BA.5.2.9
V3308 19868C>T missense_variant ORF1ab_pp1ab A6623V 7.07e-1 BA.5.3.1
V1162 4390C>T missense_variant ORF1ab_pp1a R1464W 7.07e-1 BA.5.3.3
V4312 37G>T missense_variant ORF3a V13L 7.07e-1 BA.5.3.3
V6113 1782T>C synonymous_variant ORF1ab_pp1a N594N 7.07e-1 BA.5.3.3
V6390 3789T>C synonymous_variant ORF1ab_pp1a L1263L 7.07e-1 BA.5.3.3
V8396 19260C>T synonymous_variant ORF1ab_pp1ab L6420L 7.07e-1 BA.5.3.3
V150 140A>G missense_variant ORF1ab_pp1a K47R 1.00e+0 BA.5.3.4
V2751 15804G>T missense_variant ORF1ab_pp1ab E5268D 1.00e+0 BA.5.3.4
V3824 1037G>C missense_variant S R346T 7.07e-1 BA.5.3.4
V4088 2464C>T missense_variant S L822F 7.07e-1 BA.5.3.4
V4395 154C>T missense_variant ORF3a L52F 1.00e+0 BA.5.3.4
V4664 31A>G missense_variant E T11A 1.00e+0 BA.5.3.4
V5029 55T>C missense_variant ORF7b F19L 1.00e+0 BA.5.3.4
V5073 22G>T stop_gained ORF8 G8* 1.00e+0 BA.5.3.4
V5850 99C>T synonymous_variant ORF1ab_pp1a D33D 1.00e+0 BA.5.3.4
V9139 24C>T synonymous_variant ORF3a F8F 1.00e+0 BA.5.3.4
V48 -92G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 BA.5.7
V9275 144C>T synonymous_variant E N48N 8.16e-1 BA.5.7
V8015 16411C>T synonymous_variant ORF1ab_pp1ab L5471L 6.67e-1 BA.5
V4617 757T>C missense_variant ORF3a S253P 1.00e+0 BE.1.1.1
V7291 10755C>T synonymous_variant ORF1ab_pp1a L3585L 7.07e-1 BE.1.1.1
V3721 623C>T missense_variant S T208M 6.54e-1 BF.11
V5717 109C>T missense_variant ORF10 L37F 6.25e-1 BF.14
V9191 300C>T synonymous_variant ORF3a G100G 8.02e-1 BF.14
V9470 261C>T synonymous_variant ORF7a F87F 7.90e-1 BF.14
V5968 702T>C synonymous_variant ORF1ab_pp1a H234H 7.07e-1 BF.21
V3763 733C>T missense_variant S H245Y 8.16e-1 BF.2
V411 1061C>T missense_variant ORF1ab_pp1a A354V 8.16e-1 BF.2
V6697 6082C>T synonymous_variant ORF1ab_pp1a L2028L 8.16e-1 BF.7.4.2
V2374 12521C>T missense_variant ORF1ab_pp1a T4174I 8.46e-1 BF.8
V5405 481C>T missense_variant N L161F 8.77e-1 BF.8
V8267 18306C>T synonymous_variant ORF1ab_pp1ab L6102L 9.20e-1 BF.8
V1034 3544C>T missense_variant ORF1ab_pp1a L1182F 7.07e-1 B
V8945 2469C>T synonymous_variant S F823F 7.07e-1 B
V1117 3940G>A missense_variant ORF1ab_pp1a A1314T 7.07e-1 BM.1.1.1
V2333 12214G>A missense_variant ORF1ab_pp1a V4072I 7.07e-1 BM.1.1.1
V5010 7G>C missense_variant ORF7b E3Q 7.07e-1 BM.1.1.1
V6455 4296G>A synonymous_variant ORF1ab_pp1a A1432A 7.06e-1 BN.1.2.1
V8030 16566C>T synonymous_variant ORF1ab_pp1ab Y5522Y 1.00e+0 BN.1.2.1
V9537 222C>T synonymous_variant ORF8 I74I 7.06e-1 BN.1.2.1
V4027 2050G>A missense_variant S A684T 1.00e+0 BN.1.3.1
V4779 437G>A missense_variant M R146H 1.00e+0 BN.1.3.1
V564 1652C>T missense_variant ORF1ab_pp1a T551I 8.66e-1 BQ.1.1.13
V1870 8717C>T missense_variant ORF1ab_pp1a T2906I 6.42e-1 BQ.1.1.20
V3158 18754C>T missense_variant ORF1ab_pp1ab P6252S 8.16e-1 BQ.1.1.22
V1839 8567C>T missense_variant ORF1ab_pp1a A2856V 1.00e+0 BQ.1.14
V2773 16078T>C missense_variant ORF1ab_pp1ab S5360P 7.07e-1 BQ.1.1.6
V7211 10122T>C synonymous_variant ORF1ab_pp1a T3374T 7.07e-1 BQ.1.1.6
V8375 19062A>G synonymous_variant ORF1ab_pp1ab P6354P 7.07e-1 BQ.1.1.6
V5666 -15G>T upstream_gene_variant ORF10 None 1.00e+0 C.16
V1975 9663G>T missense_variant ORF1ab_pp1a M3221I 6.32e-1 C.36
V4524 463G>T missense_variant ORF3a D155Y 6.32e-1 C.36
V6077 1548T>A synonymous_variant ORF1ab_pp1a A516A 6.32e-1 C.36
V7291 10755C>T synonymous_variant ORF1ab_pp1a L3585L 6.69e-1 C.36
V8260 18222C>T synonymous_variant ORF1ab_pp1ab L6074L 6.32e-1 C.36
V9455 210C>T synonymous_variant ORF7a G70G 7.74e-1 C.36
V9622 327T>C synonymous_variant N Y109Y 6.32e-1 C.36
V2400 12659C>T missense_variant ORF1ab_pp1a P4220L 1.00e+0 CA.3
V3062 18137C>T missense_variant ORF1ab_pp1ab P6046L 1.00e+0 CA.3
V9812 1242T>C synonymous_variant N A414A 1.00e+0 CA.3
V6219 2445C>T synonymous_variant ORF1ab_pp1a L815L 7.07e-1 CH.1.1.3
V5412 502C>T missense_variant N P168S 7.06e-1 CH.1.1
V6219 2445C>T synonymous_variant ORF1ab_pp1a L815L 9.35e-1 CH.1.1
V7966 16059C>T synonymous_variant ORF1ab_pp1ab C5353C 7.46e-1 CH.1.1
V5639 1193C>T missense_variant N A398V 1.00e+0 P.1.2
V3608 284C>T missense_variant S T95I 1.00e+0 P.1.7.1
V7035 8808C>T synonymous_variant ORF1ab_pp1a T2936T 1.00e+0 P.1.7.1
V1184 4544C>T missense_variant ORF1ab_pp1a S1515F 8.94e-1 Q.1
V4844 -4G>T upstream_gene_variant ORF7a None 6.32e-1 Q.1
V7097 9255C>T synonymous_variant ORF1ab_pp1a F3085F 1.00e+0 Q.2
V4894 118T>C missense_variant ORF7a Y40H 1.00e+0 XBB.1.2
V5107 97G>T missense_variant ORF8 V33F 1.00e+0 XBB.1.2
V1530 6431C>T missense_variant ORF1ab_pp1a P2144L 1.00e+0 XB
V4260 3679A>G missense_variant S I1227V 1.00e+0 XB
V8640 159C>T synonymous_variant S D53D 1.00e+0 XB
V1268 4965G>T missense_variant ORF1ab_pp1a K1655N 1.00e+0 A.19
V1331 5452C>T missense_variant ORF1ab_pp1a H1818Y 1.00e+0 A.19
V3484 21040C>A missense_variant ORF1ab_pp1ab R7014S 1.00e+0 A.19
V3486 21041G>A missense_variant ORF1ab_pp1ab R7014H 1.00e+0 A.19
V4011 2025G>T missense_variant S Q675H 1.00e+0 A.19
V4521 452C>T missense_variant ORF3a T151I 1.00e+0 A.19
V5512 702G>C missense_variant N M234I 1.00e+0 A.19
V6703 6099G>A synonymous_variant ORF1ab_pp1a A2033A 1.00e+0 A.19
V7506 12528G>A synonymous_variant ORF1ab_pp1a K4176K 1.00e+0 A.19
V9259 819G>T synonymous_variant ORF3a V273V 1.00e+0 A.19
V2036 10183C>T missense_variant ORF1ab_pp1a P3395S -1.00e+0 AG.1
V8268 18312C>T synonymous_variant ORF1ab_pp1ab D6104D -6.12e-1 AG.1
V6362 3522C>T synonymous_variant ORF1ab_pp1a Y1174Y 7.06e-1 AY.5.1
V8384 19152A>G synonymous_variant ORF1ab_pp1ab V6384V 7.06e-1 AY.5.1
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F 7.67e-1 B.1.1.133
V2315 12041A>G missense_variant ORF1ab_pp1a K4014R 6.42e-1 B.1.1.133
V3375 20255A>G missense_variant ORF1ab_pp1ab D6752G 1.00e+0 B.1.1.133
V4067 2306G>T missense_variant S G769V 1.00e+0 B.1.1.133
V4346 91G>A missense_variant ORF3a A31T 8.62e-1 B.1.1.133
V6859 7410G>T synonymous_variant ORF1ab_pp1a A2470A 7.67e-1 B.1.1.133
V8725 708T>C synonymous_variant S T236T 8.62e-1 B.1.1.133
V135 89G>C missense_variant ORF1ab_pp1a G30A 9.90e-1 B.1.1.159
V1790 8307G>T missense_variant ORF1ab_pp1a W2769C 6.41e-1 B.1.1.159
V5653 1240G>T missense_variant N A414S 9.80e-1 B.1.1.159
V7766 14460C>T synonymous_variant ORF1ab_pp1ab F4820F 8.14e-1 B.1.1.161
V4222 3484C>T missense_variant S P1162S 1.00e+0 B.1.1.171
V5348 214G>C missense_variant N V72L 1.00e+0 B.1.1.171
V81 -47G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.1.171
V347 812C>T missense_variant ORF1ab_pp1a P271L 1.00e+0 B.1.1.236
V2384 12544C>T missense_variant ORF1ab_pp1a L4182F 7.06e-1 B.1.1.274
V3927 1501A>T missense_variant S N501Y 7.06e-1 B.1.1.274
V4043 2102C>T missense_variant S A701V 1.00e+0 B.1.1.274
V1249 4850C>T missense_variant ORF1ab_pp1a T1617I 1.00e+0 B.1.1.302
V1863 8672C>T missense_variant ORF1ab_pp1a A2891V 1.00e+0 B.1.1.302
V4610 719C>T missense_variant ORF3a P240L 1.00e+0 B.1.1.302
V6636 5604C>T synonymous_variant ORF1ab_pp1a Y1868Y 1.00e+0 B.1.1.302
V5072 22G>A missense_variant ORF8 G8R 8.90e-1 B.1.1.322
V9557 360C>T synonymous_variant ORF8 F120F 7.91e-1 B.1.1.322
V8449 19719C>T synonymous_variant ORF1ab_pp1ab V6573V 1.00e+0 B.1.1.328
V2277 11788C>T missense_variant ORF1ab_pp1a L3930F -6.88e-1 B.1.1.332
V4232 3526G>T missense_variant S V1176F -6.88e-1 B.1.1.332
V4823 98T>C missense_variant ORF6 I33T 6.88e-1 B.1.1.332
V5556 875T>C missense_variant N I292T 6.88e-1 B.1.1.332
V6313 3165A>G synonymous_variant ORF1ab_pp1a T1055T 7.24e-1 B.1.1.332
V2865 16794G>T missense_variant ORF1ab_pp1ab M5598I 7.02e-1 B.1.1.375
V4406 171G>T missense_variant ORF3a Q57H 7.02e-1 B.1.1.375
V5794 *4371G>T downstream_gene_variant S None 1.00e+0 B.1.1.375
V6830 7128G>T synonymous_variant ORF1ab_pp1a P2376P 1.00e+0 B.1.1.375
V7744 14335C>T synonymous_variant ORF1ab_pp1ab L4779L 1.00e+0 B.1.1.375
V9511 51C>T synonymous_variant ORF8 H17H 1.00e+0 B.1.1.375
V9776 1023C>T synonymous_variant N D341D 1.00e+0 B.1.1.375
V3781 761C>T missense_variant S S254F 1.00e+0 B.1.1.385
V504 1405C>T missense_variant ORF1ab_pp1a L469F 1.00e+0 B.1.1.385
V1530 6431C>T missense_variant ORF1ab_pp1a P2144L 7.06e-1 B.1.1.398
V2853 16744A>G missense_variant ORF1ab_pp1ab I5582V 1.00e+0 B.1.1.398
V3001 17819T>C missense_variant ORF1ab_pp1ab I5940T 1.00e+0 B.1.1.398
V3090 18304C>T missense_variant ORF1ab_pp1ab L6102F 1.00e+0 B.1.1.398
V4624 766_769delGTTA frameshift_variant ORF3a V256fs 1.00e+0 B.1.1.398
V5317 100G>T missense_variant N G34W 1.00e+0 B.1.1.398
V7254 10452T>C synonymous_variant ORF1ab_pp1a N3484N 1.00e+0 B.1.1.398
V7962 16011A>G synonymous_variant ORF1ab_pp1ab S5337S 1.00e+0 B.1.1.398
V8588 20970C>T synonymous_variant ORF1ab_pp1ab A6990A 1.00e+0 B.1.1.398
V8946 2472C>T synonymous_variant S N824N 7.06e-1 B.1.1.398
V1665 7484C>T missense_variant ORF1ab_pp1a T2495I 8.14e-1 B.1.1.409
V3526 35C>T missense_variant S S12F 8.14e-1 B.1.1.409
V3657 443A>C missense_variant S N148T 8.14e-1 B.1.1.409
V4669 61C>T missense_variant E L21F 8.14e-1 B.1.1.409
V6356 3471C>T synonymous_variant ORF1ab_pp1a D1157D 8.14e-1 B.1.1.409
V6833 7155C>T synonymous_variant ORF1ab_pp1a I2385I 8.14e-1 B.1.1.409
V7540 12780G>A synonymous_variant ORF1ab_pp1a V4260V 8.14e-1 B.1.1.409
V7541 12786C>T synonymous_variant ORF1ab_pp1a A4262A 6.61e-1 B.1.1.409
V1441 6136C>T missense_variant ORF1ab_pp1a P2046S 1.00e+0 B.1.1.44
V65 -64T>C upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.1.44
V6939 8025C>T synonymous_variant ORF1ab_pp1a L2675L 1.00e+0 B.1.1.44
V7169 9771C>T synonymous_variant ORF1ab_pp1a I3257I 1.00e+0 B.1.1.44
V5440 578G>C missense_variant N S193T 1.00e+0 B.1.1.46
V5783 *4361G>T downstream_gene_variant S None 1.00e+0 B.1.1.46
V6430 4080C>T synonymous_variant ORF1ab_pp1a I1360I 7.05e-1 B.1.1.46
V6564 5037A>G synonymous_variant ORF1ab_pp1a A1679A 7.05e-1 B.1.1.46
V8460 19827C>T synonymous_variant ORF1ab_pp1ab P6609P 7.05e-1 B.1.1.46
V9301 103C>T synonymous_variant M L35L 1.00e+0 B.1.1.46
V9494 49C>T synonymous_variant ORF7b L17L 7.05e-1 B.1.1.46
V9567 48G>A synonymous_variant N T16T 7.05e-1 B.1.1.46
V4286 3774A>C missense_variant S E1258D 1.00e+0 B.1.1.517
V4287 3775G>C missense_variant S D1259H 1.00e+0 B.1.1.517
V4939 226C>T stop_gained ORF7a Q76* 1.00e+0 B.1.1.517
V5110 103G>T missense_variant ORF8 D35Y 1.00e+0 B.1.1.517
V540 1586T>C missense_variant ORF1ab_pp1a I529T 1.00e+0 B.1.1.517
V6182 2220C>T synonymous_variant ORF1ab_pp1a I740I 1.00e+0 B.1.1.517
V7445 11976C>T synonymous_variant ORF1ab_pp1a D3992D 1.00e+0 B.1.1.517
V8396 19260C>T synonymous_variant ORF1ab_pp1ab L6420L 1.00e+0 B.1.1.517
V1084 3730G>A missense_variant ORF1ab_pp1a E1244K 1.00e+0 B.1.1.521
V1414 6047C>T missense_variant ORF1ab_pp1a T2016I 7.05e-1 B.1.1.521
V2104 10760T>C missense_variant ORF1ab_pp1a I3587T 1.00e+0 B.1.1.521
V5668 -13C>T upstream_gene_variant ORF10 None 1.00e+0 B.1.1.521
V8451 19752C>T synonymous_variant ORF1ab_pp1ab D6584D 1.00e+0 B.1.1.521
V2043 10295C>T missense_variant ORF1ab_pp1a T3432I 1.00e+0 B.1.1.522
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F 1.00e+0 B.1.160.28
V8897 2046G>A synonymous_variant S R682R 1.00e+0 B.1.160.28
V9407 96C>T synonymous_variant ORF6 I32I 1.00e+0 B.1.160.28
V302 578C>T missense_variant ORF1ab_pp1a P193L 1.00e+0 B.1.177.23
V3033 17983C>T missense_variant ORF1ab_pp1ab P5995S 1.00e+0 B.1.177.23
V8856 1785C>T synonymous_variant S V595V 1.00e+0 B.1.177.23
V7017 8622A>G synonymous_variant ORF1ab_pp1a L2874L 1.00e+0 B.1.189
V3259 19598C>T missense_variant ORF1ab_pp1ab A6533V 6.31e-1 B.1.210
V4419 193C>T missense_variant ORF3a L65F 9.53e-1 B.1.210
V5144 184G>T missense_variant ORF8 V62L 9.56e-1 B.1.210
V5443 581C>T missense_variant N S194L 7.32e-1 B.1.210
V5875 222G>T synonymous_variant ORF1ab_pp1a S74S 9.77e-1 B.1.210
V6029 1176C>T synonymous_variant ORF1ab_pp1a G392G 9.29e-1 B.1.210
V7174 9786G>A synonymous_variant ORF1ab_pp1a L3262L 6.59e-1 B.1.210
V929 3146C>T missense_variant ORF1ab_pp1a A1049V 9.29e-1 B.1.210
V9325 300C>T synonymous_variant M F100F 9.78e-1 B.1.210
V3411 20495C>T missense_variant ORF1ab_pp1ab A6832V 1.00e+0 B.1.256
V342 794C>T missense_variant ORF1ab_pp1a T265I 1.00e+0 B.1.256
V4355 104T>C missense_variant ORF3a I35T 1.00e+0 B.1.256
V4406 171G>T missense_variant ORF3a Q57H 1.00e+0 B.1.256
V4524 463G>T missense_variant ORF3a D155Y 8.62e-1 B.1.256
V5422 539G>C missense_variant N S180T 1.00e+0 B.1.256
V6528 4797G>A synonymous_variant ORF1ab_pp1a L1599L 1.00e+0 B.1.256
V6530 4803A>G synonymous_variant ORF1ab_pp1a G1601G 1.00e+0 B.1.256
V6799 6840C>T synonymous_variant ORF1ab_pp1a T2280T 8.13e-1 B.1.256
V7423 11811C>T synonymous_variant ORF1ab_pp1a N3937N 1.00e+0 B.1.256
V8149 17439C>T synonymous_variant ORF1ab_pp1ab N5813N 1.00e+0 B.1.256
V9272 91C>T synonymous_variant E L31L 1.00e+0 B.1.256
V9731 852A>G synonymous_variant N G284G 1.00e+0 B.1.256
V205 274C>T missense_variant ORF1ab_pp1a L92F -6.35e-1 B.1.293
V3411 20495C>T missense_variant ORF1ab_pp1ab A6832V 6.41e-1 B.1.293
V6489 4530C>T synonymous_variant ORF1ab_pp1a S1510S -6.35e-1 B.1.293
V7682 13914C>T synonymous_variant ORF1ab_pp1ab T4638T -6.35e-1 B.1.293
V3211 19138C>T missense_variant ORF1ab_pp1ab H6380Y 7.05e-1 B.1.397
V4524 463G>T missense_variant ORF3a D155Y 1.00e+0 B.1.397
V5759 *4349C>T downstream_gene_variant S None 7.05e-1 B.1.397
V5779 *4359C>T downstream_gene_variant S None 7.05e-1 B.1.397
V5897 318C>T synonymous_variant ORF1ab_pp1a V106V 7.05e-1 B.1.397
V5992 903A>G synonymous_variant ORF1ab_pp1a R301R 7.05e-1 B.1.397
V6014 1023C>T synonymous_variant ORF1ab_pp1a C341C 6.27e-1 B.1.397
V6245 2616C>T synonymous_variant ORF1ab_pp1a A872A 1.00e+0 B.1.397
V6367 3552C>T synonymous_variant ORF1ab_pp1a D1184D 7.05e-1 B.1.397
V6689 6021C>T synonymous_variant ORF1ab_pp1a T2007T 1.00e+0 B.1.397
V6774 6676C>T synonymous_variant ORF1ab_pp1a L2226L 1.00e+0 B.1.397
V7105 9327C>T synonymous_variant ORF1ab_pp1a Y3109Y 7.05e-1 B.1.397
V8296 18492G>T synonymous_variant ORF1ab_pp1ab P6164P 7.05e-1 B.1.397
V9602 168C>T synonymous_variant N L56L 7.05e-1 B.1.397
V3351 20141C>T missense_variant ORF1ab_pp1ab P6714L 1.00e+0 B.1.408
V5773 *4355C>T downstream_gene_variant S None 8.49e-1 B.1.408
V7291 10755C>T synonymous_variant ORF1ab_pp1a L3585L 7.95e-1 B.1.408
V9429 91T>C synonymous_variant ORF7a L31L 9.52e-1 B.1.408
V9764 981G>T synonymous_variant N S327S 1.00e+0 B.1.408
V981 3337C>T missense_variant ORF1ab_pp1a H1113Y 1.00e+0 B.1.408
V3593 227C>T missense_variant S T76I 7.06e-1 B.1.411
V4546 524C>T missense_variant ORF3a T175I 7.06e-1 B.1.411
V7125 9537G>T synonymous_variant ORF1ab_pp1a A3179A 1.00e+0 B.1.411
V1982 9764C>T missense_variant ORF1ab_pp1a T3255I 1.00e+0 B.1.562
V2485 13448A>G missense_variant ORF1ab_pp1ab K4483R 1.00e+0 B.1.562
V3559 86C>T missense_variant S T29I 1.00e+0 B.1.562
V5594 1075G>T missense_variant N A359S 1.00e+0 B.1.562
V5727 *4306G>T downstream_gene_variant S None 1.00e+0 B.1.562
V6228 2517G>T synonymous_variant ORF1ab_pp1a V839V 1.00e+0 B.1.562
V8292 18480C>T synonymous_variant ORF1ab_pp1ab Y6160Y 1.00e+0 B.1.562
V8336 18768C>T synonymous_variant ORF1ab_pp1ab D6256D 1.00e+0 B.1.562
V9741 894C>T synonymous_variant N Y298Y 1.00e+0 B.1.562
V221 328C>T missense_variant ORF1ab_pp1a H110Y 1.00e+0 B.1.596.1
V6574 5100C>T synonymous_variant ORF1ab_pp1a Y1700Y 1.00e+0 B.1.596.1
V7421 11805G>T synonymous_variant ORF1ab_pp1a L3935L 1.00e+0 B.1.596.1
V8236 18102A>G synonymous_variant ORF1ab_pp1ab L6034L 1.00e+0 B.1.596.1
V8300 18540C>T synonymous_variant ORF1ab_pp1ab S6180S 1.00e+0 B.1.596.1
V2952 17422G>T missense_variant ORF1ab_pp1ab V5808F 1.00e+0 BA.4.8
V3519 8T>G missense_variant S V3G 7.04e-1 BA.4.8
V6182 2220C>T synonymous_variant ORF1ab_pp1a I740I 1.00e+0 BA.4.8
V7358 11409C>T synonymous_variant ORF1ab_pp1a Y3803Y 7.04e-1 BA.4.8
V9509 30C>T synonymous_variant ORF8 I10I 1.00e+0 BA.5.1.20
V3592 224G>T missense_variant S G75V 8.15e-1 BL.3
V1013 3463G>T missense_variant ORF1ab_pp1a G1155C 1.00e+0 BQ.2
V6957 8121C>T synonymous_variant ORF1ab_pp1a H2707H 1.00e+0 BQ.2
V1682 7586C>T missense_variant ORF1ab_pp1a A2529V 1.00e+0 C.11
V5397 452C>T missense_variant N P151L 1.00e+0 C.11
V8010 16383G>A synonymous_variant ORF1ab_pp1ab T5461T 1.00e+0 C.11
V9233 666C>T synonymous_variant ORF3a D222D 1.00e+0 C.11
V5540 799G>T missense_variant N A267S 1.00e+0 C.14
V1219 4700C>T missense_variant ORF1ab_pp1a T1567I 7.06e-1 C.1
V3304 19838G>T missense_variant ORF1ab_pp1ab S6613I 7.06e-1 C.1
V7035 8808C>T synonymous_variant ORF1ab_pp1a T2936T 7.06e-1 C.1
V8927 2334C>T synonymous_variant S T778T 1.00e+0 C.1
V8944 2461C>T synonymous_variant S L821L 7.06e-1 C.1
V123 70C>T missense_variant ORF1ab_pp1a R24C 7.81e-1 C.26
V1414 6047C>T missense_variant ORF1ab_pp1a T2016I 7.68e-1 C.26
V1980 9731C>T missense_variant ORF1ab_pp1a S3244L 7.68e-1 C.26
V4564 578G>T missense_variant ORF3a W193L 6.59e-1 C.26
V5803 *4380G>A downstream_gene_variant S None 7.09e-1 C.26
V85 -44C>T upstream_gene_variant ORF1ab_pp1a None 7.81e-1 C.26
V2116 10818G>T missense_variant ORF1ab_pp1a L3606F 7.06e-1 CM.5
V393 998C>T missense_variant ORF1ab_pp1a T333M 7.06e-1 CM.5
V7622 13356C>T synonymous_variant ORF1ab_pp1ab D4452D 8.15e-1 CM.5
V8901 2049G>T synonymous_variant S R683R 7.06e-1 CM.5
V5343 200C>T missense_variant N P67L 1.00e+0 XBB.2.2
V6383 3744C>T synonymous_variant ORF1ab_pp1a F1248F 1.00e+0 XBB.2.2
V7207 10074T>C synonymous_variant ORF1ab_pp1a N3358N 1.00e+0 XBB.2.2
V8902 2073C>T synonymous_variant S S691S 1.00e+0 XBB.2.2
V1004 3427G>T missense_variant ORF1ab_pp1a V1143F 1.00e+0 XBE
V4842 -5C>T upstream_gene_variant ORF7a None 1.00e+0 XBE
V5904 348G>A synonymous_variant ORF1ab_pp1a V116V 1.00e+0 XBE
V6426 4056C>T synonymous_variant ORF1ab_pp1a A1352A -7.05e-1 XBE





Manual curation of mutation (15642G>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