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The current mutation

ID: V6828
DNA: 7125C>T
Protein: A2375A
Position: 7390








COV2Var annotation categories







Summary information of mutation (7125C>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   7390
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   synonymous_variant
  DNA Level   DNA Mutation: 7125C>T
  Ref Seq: C
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: A2375A
  Protein 3-letter Mutation: Ala2375Ala

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 (7125C>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.1.221 67 42 6.27e-1
2020-10 B.1.1.28 67 5 7.46e-2
2020-10 B.1 67 4 5.97e-2
2020-11 B.1.221.4 54 20 3.70e-1
2020-11 B.1.221 54 18 3.33e-1
2020-11 B.1 54 7 1.30e-1
2020-12 B.1.221.4 126 52 4.13e-1
2020-12 B.1.2 126 18 1.43e-1
2020-12 B.1 126 16 1.27e-1
2020-03 B 11 6 5.45e-1
2020-03 B.1.139 11 2 1.82e-1
2020-03 B.1 11 1 9.09e-2
2020-04 B.1.263 17 8 4.71e-1
2020-04 B.40 17 5 2.94e-1
2020-04 B.1 17 2 1.18e-1
2020-05 B.1.1.25 4 1 2.50e-1
2020-05 B.1.263 4 1 2.50e-1
2020-05 B.1.390 4 1 2.50e-1
2020-06 B.1 14 11 7.86e-1
2020-06 B.1.1.1 14 1 7.14e-2
2020-06 B.1.540 14 1 7.14e-2
2020-07 B.1 14 9 6.43e-1
2020-07 B.1.1.485 14 2 1.43e-1
2020-07 B.1.614 14 2 1.43e-1
2020-08 B.1 19 12 6.32e-1
2020-08 B.1.1.326 19 5 2.63e-1
2020-08 B.1.1.28 19 1 5.26e-2
2020-09 B.1.221 58 28 4.83e-1
2020-09 D.2 58 12 2.07e-1
2020-09 B.1.1.326 58 7 1.21e-1
2021-01 B.1.221.4 245 77 3.14e-1
2021-01 B.1.1.333 245 41 1.67e-1
2021-01 B.1.1.7 245 21 8.57e-2
2021-10 AY.6 345 88 2.55e-1
2021-10 AY.4 345 81 2.35e-1
2021-10 AY.103 345 49 1.42e-1
2021-11 AY.4 642 232 3.61e-1
2021-11 AY.43 642 68 1.06e-1
2021-11 AY.103 642 61 9.50e-2
2021-12 AY.4 422 126 2.99e-1
2021-12 AY.43 422 47 1.11e-1
2021-12 AY.103 422 43 1.02e-1
2021-02 B.1.1.7 333 195 5.86e-1
2021-02 B.1.221.4 333 58 1.74e-1
2021-02 B.1.1.205 333 14 4.20e-2
2021-03 B.1.1.7 373 306 8.20e-1
2021-03 B.1.429 373 15 4.02e-2
2021-03 B.1.221.4 373 9 2.41e-2
2021-04 B.1.1.7 307 284 9.25e-1
2021-04 B.1 307 5 1.63e-2
2021-04 B.1.429 307 4 1.30e-2
2021-05 B.1.1.7 204 177 8.68e-1
2021-05 B.1.617.2 204 7 3.43e-2
2021-05 B.1.466.2 204 5 2.45e-2
2021-06 B.1.617.2 246 110 4.47e-1
2021-06 AY.38 246 52 2.11e-1
2021-06 B.1.1.7 246 52 2.11e-1
2021-07 AY.38 218 67 3.07e-1
2021-07 B.1.617.2 218 48 2.20e-1
2021-07 AY.9.2 218 40 1.83e-1
2021-08 AY.29 285 66 2.32e-1
2021-08 AY.38 285 47 1.65e-1
2021-08 AY.4 285 37 1.30e-1
2021-09 AY.6 383 115 3.00e-1
2021-09 AY.4 383 105 2.74e-1
2021-09 AY.29 383 28 7.31e-2
2022-01 BA.1.1 174 39 2.24e-1
2022-01 BA.1 174 30 1.72e-1
2022-01 BA.1.15 174 15 8.62e-2
2022-10 BA.5.9 48 10 2.08e-1
2022-10 BF.10 48 8 1.67e-1
2022-10 BF.7 48 5 1.04e-1
2022-11 CK.2 64 8 1.25e-1
2022-11 BF.7.15 64 6 9.38e-2
2022-11 XBB 64 6 9.38e-2
2022-12 BQ.1.1 74 8 1.08e-1
2022-12 BA.5.2.6 74 7 9.46e-2
2022-12 BF.7.6 74 7 9.46e-2
2022-02 BA.1.1 247 128 5.18e-1
2022-02 BA.1 247 44 1.78e-1
2022-02 BA.2 247 25 1.01e-1
2022-03 BA.2 143 74 5.17e-1
2022-03 BA.1.1 143 23 1.61e-1
2022-03 BA.1 143 11 7.69e-2
2022-04 BA.2 108 57 5.28e-1
2022-04 BA.2.3 108 13 1.20e-1
2022-04 BA.2.9 108 10 9.26e-2
2022-05 BA.2 117 49 4.19e-1
2022-05 BA.2.9 117 16 1.37e-1
2022-05 BA.4.1 117 12 1.03e-1
2022-06 BA.2 81 15 1.85e-1
2022-06 BA.4.1 81 9 1.11e-1
2022-06 BA.2.12 81 8 9.88e-2
2022-07 BA.5.5 137 61 4.45e-1
2022-07 BA.2.3 137 15 1.09e-1
2022-07 BA.4.4 137 11 8.03e-2
2022-08 BA.5.5 80 14 1.75e-1
2022-08 BA.5 80 9 1.12e-1
2022-08 BA.5.1.17 80 9 1.12e-1
2022-09 BA.5.1.3 55 13 2.36e-1
2022-09 BF.10 55 7 1.27e-1
2022-09 BF.21 55 5 9.09e-2
2023-01 BQ.1.1 57 7 1.23e-1
2023-01 XBB.1.5 57 6 1.05e-1
2023-01 BA.5.2.6 57 4 7.02e-2
2023-02 XBB.1.5 27 6 2.22e-1
2023-02 CH.1.1.1 27 4 1.48e-1
2023-02 BF.7.15 27 2 7.41e-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
V6828 AY.6 1.05e-2 291 2021-3-16 2022-5-23
V6828 AY.38 1.03e-1 192 2020-7-16 2022-5-9
V6828 B.1.1.326 2.95e-2 16 2020-3-23 2021-9-11
V6828 B.1.1.333 6.51e-2 63 2020-1-29 2021-5-13
V6828 B.1.1.205 4.00e-2 12 2020-5-16 2021-8-8
V6828 B.1.221.4 9.16e-1 219 2020-11-2 2021-5-12
V6828 B.1.248 5.56e-2 2 2020-3-28 2021-9-29
V6828 B.1.256 2.54e-2 3 2020-3-22 2021-4-26
V6828 B.1.263 4.76e-1 10 2020-3-19 2020-11-5
V6828 B.1.478 1.59e-2 2 2020-5-15 2021-3-5
V6828 B.1.540 4.88e-2 4 2020-3-27 2021-3-15
V6828 B.1.543 3.19e-2 3 2020-8-30 2021-3-10
V6828 B.1.614 2.50e-1 2 2020-6-15 2020-7-12
V6828 B.1.639 1.11e-1 6 2021-1-19 2021-11-15
V6828 B.1.78 2.80e-2 3 2020-3-12 2021-12-9
V6828 CK.2 2.79e-2 10 2022-7-1 2023-2-15






Examining mutation (7125C>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
Odocoileus virginianus B.1.311 USA 2020-12-8 EPI_ISL_5804724
Odocoileus virginianus B.1.234 USA 2020-12-10 EPI_ISL_5804731
Odocoileus virginianus B.1.1.7 USA 2021-10-27 EPI_ISL_13658779
Odocoileus virginianus B.1.1.7 USA 2021-11-22 EPI_ISL_13610689
Odocoileus virginianus B.1.1.7 USA 2021-11-11 EPI_ISL_13610667
Odocoileus virginianus B.1.1.7 USA 2021-11-20 EPI_ISL_13658809




Association between mutation (7125C>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 6.45e+0 2.42e+0 2.66e+0 7.80e-3 Increase
Deceased -1.54e+1 1.77e+3 -8.71e-3 9.93e-1 Decrease
Homebound 3.66e-15 1.70e+5 2.15e-20 1.00e+0 Increase
Hospitalized 1.01e+0 9.87e-1 1.02e+0 3.08e-1 Increase
Mild -1.52e+1 1.05e+3 -1.44e-2 9.88e-1 Decrease
Recovered -1.58e+1 1.06e+3 -1.48e-2 9.88e-1 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 -4.11e-1 2.20e-1 -1.87e+0 6.10e-2 Decrease
18-39 -5.10e-1 1.12e-1 -4.56e+0 5.04e-6 Decrease
40-64 2.46e-1 1.05e-1 2.34e+0 1.91e-2 Increase
65-84 5.37e-1 1.46e-1 3.69e+0 2.25e-4 Increase
>=85 8.96e-1 2.67e-1 3.36e+0 7.85e-4 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 -1.62e-1 1.04e-1 -1.55e+0 1.21e-1 Decrease





Investigating natural selection at mutation (7125C>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 (7125C>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 (7125C>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 (7125C>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 (7125C>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 (7125C>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 (7125C>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 (7125C>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 (7125C>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 (7125C>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
V8890 2013C>T synonymous_variant S C671C 6.56e-1 B.1.177
V7696 13998C>T synonymous_variant ORF1ab_pp1ab D4666D 6.51e-1 AY.43
V7567 12975G>T synonymous_variant ORF1ab_pp1a S4325S 7.34e-1 AY.29
V9543 270C>T synonymous_variant ORF8 C90C 6.11e-1 BA.1.17
V9245 747C>T synonymous_variant ORF3a I249I 6.55e-1 AY.125
V4350 95C>T missense_variant ORF3a T32I 6.77e-1 AY.4.2
V1408 6030A>G missense_variant ORF1ab_pp1a I2010M 6.19e-1 AY.9.2
V1185 4550C>T missense_variant ORF1ab_pp1a S1517F 6.90e-1 B.1.617.2
V3568 162G>T missense_variant S L54F 7.07e-1 AY.101
V9213 504C>T synonymous_variant ORF3a V168V 1.00e+0 AY.101
V9807 1212C>T synonymous_variant N S404S 1.00e+0 AY.101
V4033 2062G>T missense_variant S A688S 8.66e-1 AY.104
V4626 766G>T missense_variant ORF3a V256F 7.49e-1 AY.104
V6454 4278C>T synonymous_variant ORF1ab_pp1a T1426T 7.49e-1 AY.104
V7098 9264A>G synonymous_variant ORF1ab_pp1a S3088S 8.66e-1 AY.104
V4840 181G>T missense_variant ORF6 D61Y 7.07e-1 AY.106
V9248 759C>T synonymous_variant ORF3a S253S 7.07e-1 AY.106
V3592 224G>T missense_variant S G75V 1.00e+0 AY.108
V4771 320G>A missense_variant M R107H 1.00e+0 AY.108
V7639 13557C>T synonymous_variant ORF1ab_pp1ab L4519L 1.00e+0 AY.109
V1561 6600G>T missense_variant ORF1ab_pp1a K2200N 7.07e-1 AY.113
V821 2773T>C missense_variant ORF1ab_pp1a Y925H 6.32e-1 AY.118
V5900 327T>C synonymous_variant ORF1ab_pp1a P109P 7.07e-1 AY.121
V4767 257G>T missense_variant M C86F 1.00e+0 AY.122.1
V2637 14590G>T missense_variant ORF1ab_pp1ab V4864L 1.00e+0 AY.122.5
V8172 17586C>T synonymous_variant ORF1ab_pp1ab G5862G 7.07e-1 AY.122.5
V123 70C>T missense_variant ORF1ab_pp1a R24C 7.60e-1 AY.127
V1648 7223C>T missense_variant ORF1ab_pp1a T2408I 9.69e-1 AY.127
V5937 558C>T synonymous_variant ORF1ab_pp1a V186V 7.85e-1 AY.127
V7871 15309T>C synonymous_variant ORF1ab_pp1ab D5103D 7.07e-1 AY.129
V5801 *4378C>T downstream_gene_variant S None 7.07e-1 AY.27
V1585 6772G>T missense_variant ORF1ab_pp1a G2258C 1.00e+0 AY.33.2
V5544 812C>T missense_variant N T271I 1.00e+0 AY.33.2
V5652 1238G>T missense_variant N S413I 1.00e+0 AY.33.2
V430 1135G>A missense_variant ORF1ab_pp1a G379R 8.66e-1 AY.33
V5933 540G>A synonymous_variant ORF1ab_pp1a G180G 8.66e-1 AY.33
V2845 16688C>T missense_variant ORF1ab_pp1ab T5563I 1.00e+0 AY.34.1.1
V4757 232G>T missense_variant M G78C 1.00e+0 AY.34.1.1
V3357 20164C>T missense_variant ORF1ab_pp1ab P6722S 7.07e-1 AY.34.1
V4877 74G>T missense_variant ORF7a R25I 7.07e-1 AY.34.1
V948 3218G>T missense_variant ORF1ab_pp1a G1073V 1.00e+0 AY.34.2
V8140 17379T>C synonymous_variant ORF1ab_pp1ab A5793A 8.16e-1 AY.34
V4155 3059C>T missense_variant S A1020V 1.00e+0 AY.36
V1424 6077A>G missense_variant ORF1ab_pp1a D2026G 9.59e-1 AY.38
V7757 14406C>T synonymous_variant ORF1ab_pp1ab V4802V 6.91e-1 AY.38
V9562 24T>C synonymous_variant N N8N 8.50e-1 AY.38
V5446 584G>T missense_variant N R195I 1.00e+0 AY.4.17
V2483 13439A>G missense_variant ORF1ab_pp1ab N4480S 1.00e+0 AY.42
V8496 20172C>T synonymous_variant ORF1ab_pp1ab D6724D 7.07e-1 AY.42
V2993 17756G>A missense_variant ORF1ab_pp1ab R5919K 7.07e-1 AY.46.6
V3476 20968G>A missense_variant ORF1ab_pp1ab A6990T 1.00e+0 AY.4.9
V5946 588C>T synonymous_variant ORF1ab_pp1a Y196Y 7.07e-1 AY.4.9
V8562 20784T>C synonymous_variant ORF1ab_pp1ab D6928D 1.00e+0 AY.4.9
V8384 19152A>G synonymous_variant ORF1ab_pp1ab V6384V 1.00e+0 AY.53
V1315 5357C>T missense_variant ORF1ab_pp1a P1786L 9.55e-1 AY.6
V9609 225C>T synonymous_variant N N75N 8.68e-1 AY.6
V3060 18131C>T missense_variant ORF1ab_pp1ab A6044V 7.07e-1 AY.7.1
V4473 309_311dupCCC disruptive_inframe_insertion ORF3a P104dup 1.00e+0 AY.7.1
V5772 *4354C>T downstream_gene_variant S None 7.07e-1 AY.7.1
V2031 10111C>T missense_variant ORF1ab_pp1a P3371S 6.66e-1 AY.7.2
V2520 13656G>T missense_variant ORF1ab_pp1ab K4552N 8.16e-1 AY.7.2
V8563 20790C>T synonymous_variant ORF1ab_pp1ab Y6930Y 1.00e+0 AY.7.2
V1131 4055C>T missense_variant ORF1ab_pp1a A1352V 1.00e+0 AY.73
V2754 15811G>T missense_variant ORF1ab_pp1ab D5271Y 1.00e+0 AY.73
V3072 18188C>T missense_variant ORF1ab_pp1ab A6063V 1.00e+0 AY.73
V7725 14211A>G synonymous_variant ORF1ab_pp1ab G4737G 1.00e+0 AY.73
V7867 15276C>T synonymous_variant ORF1ab_pp1ab V5092V 1.00e+0 AY.73
V2761 15914C>T missense_variant ORF1ab_pp1ab S5305L 1.00e+0 AY.77
V4251 3621G>T missense_variant S E1207D 1.00e+0 AY.77
V6125 1848C>T synonymous_variant ORF1ab_pp1a I616I 1.00e+0 AY.77
V7353 11388C>T synonymous_variant ORF1ab_pp1a L3796L 7.07e-1 AY.77
V9151 102G>T synonymous_variant ORF3a T34T 1.00e+0 AY.77
V2123 10852A>G missense_variant ORF1ab_pp1a I3618V 7.07e-1 AY.85
V4912 177_195delTAGCACTCAATTTGCTTTT frameshift_variant ORF7a F59fs 7.07e-1 AY.85
V8644 174C>T synonymous_variant S F58F 7.07e-1 AY.91
V2154 11001G>T missense_variant ORF1ab_pp1a L3667F 8.16e-1 AY.92
V842 2831C>T missense_variant ORF1ab_pp1a S944L 7.30e-1 AY.92
V3744 646C>T missense_variant S L216F 1.00e+0 AY.94
V6792 6810T>C synonymous_variant ORF1ab_pp1a Y2270Y 1.00e+0 AY.94
V7801 14691A>G synonymous_variant ORF1ab_pp1ab P4897P 1.00e+0 AY.99.1
V6577 5127C>T synonymous_variant ORF1ab_pp1a N1709N 1.00e+0 AY.99
V7358 11409C>T synonymous_variant ORF1ab_pp1a Y3803Y 1.00e+0 AY.99
V8843 1686C>T synonymous_variant S F562F 1.00e+0 AY.99
V3003 17824G>A missense_variant ORF1ab_pp1ab G5942R 7.07e-1 AY.9
V2942 17351A>G missense_variant ORF1ab_pp1ab K5784R 1.00e+0 B.1.1.1
V6008 990A>G synonymous_variant ORF1ab_pp1a S330S 1.00e+0 B.1.1.1
V4350 95C>T missense_variant ORF3a T32I 1.00e+0 B.1.1.263
V5101 88C>T missense_variant ORF8 P30S 1.00e+0 B.1.1.263
V7592 13152T>C synonymous_variant ORF1ab_pp1a D4384D 1.00e+0 B.1.1.263
V3500 21176C>T missense_variant ORF1ab_pp1ab S7059F 8.25e-1 B.1.1.28
V4256 3656G>T missense_variant S G1219V 7.39e-1 B.1.1.28
V5014 14C>T missense_variant ORF7b S5L 8.43e-1 B.1.1.28
V6226 2499G>T synonymous_variant ORF1ab_pp1a V833V 8.04e-1 B.1.1.28
V6537 4875C>T synonymous_variant ORF1ab_pp1a D1625D 6.88e-1 B.1.1.28
V1314 5356C>T missense_variant ORF1ab_pp1a P1786S 1.00e+0 B.1.1.294
V8666 273T>C synonymous_variant S Y91Y 7.86e-1 B.1.1.326
V9358 429G>T synonymous_variant M V143V 7.15e-1 B.1.1.326
V2021 10058A>G missense_variant ORF1ab_pp1a K3353R 6.17e-1 B.1.1.333
V3781 761C>T missense_variant S S254F 8.66e-1 B.1.177.21
V1528 6428A>G missense_variant ORF1ab_pp1a K2143R 1.00e+0 B.1.177.81
V1980 9731C>T missense_variant ORF1ab_pp1a S3244L 7.07e-1 B.1.177.82
V6832 7152C>T synonymous_variant ORF1ab_pp1a Y2384Y 7.07e-1 B.1.234
V8046 16686T>C synonymous_variant ORF1ab_pp1ab P5562P 7.07e-1 B.1.234
V514 1445C>T missense_variant ORF1ab_pp1a A482V 1.00e+0 B.1.349
V7818 14859T>C synonymous_variant ORF1ab_pp1ab S4953S 1.00e+0 B.1.349
V1254 4885G>T missense_variant ORF1ab_pp1a V1629F 8.66e-1 B.1.36.29
V1949 9413T>C missense_variant ORF1ab_pp1a F3138S 1.00e+0 B.1.36.29
V3797 790G>T missense_variant S A264S 8.16e-1 B.1.36.29
V2027 10076C>T missense_variant ORF1ab_pp1a P3359L 7.07e-1 B.1.362
V24 -161G>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 B.1.362
V359 876G>T missense_variant ORF1ab_pp1a K292N 7.07e-1 B.1.362
V4817 80G>T missense_variant ORF6 W27L 7.07e-1 B.1.362
V697 2180C>T missense_variant ORF1ab_pp1a T727I 7.07e-1 B.1.362
V7510 12555A>G synonymous_variant ORF1ab_pp1a L4185L 7.07e-1 B.1.362
V3600 239A>G missense_variant S D80G 1.00e+0 B.1.36
V1539 6461C>T missense_variant ORF1ab_pp1a T2154I 1.00e+0 B.1.396
V2815 16469C>T missense_variant ORF1ab_pp1ab S5490L 1.00e+0 B.1.396
V2849 16721C>T missense_variant ORF1ab_pp1ab T5574I 1.00e+0 B.1.400
V4710 -14C>T upstream_gene_variant M None 1.00e+0 B.1.400
V8132 17286C>T synonymous_variant ORF1ab_pp1ab L5762L 7.07e-1 B.1.400
V8307 18564C>T synonymous_variant ORF1ab_pp1ab V6188V 1.00e+0 B.1.400
V3091 18319G>A missense_variant ORF1ab_pp1ab V6107I 1.00e+0 B.1.416.1
V67 -62G>A upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.416.1
V2770 15983C>T missense_variant ORF1ab_pp1ab A5328V 8.16e-1 B.1.509
V2986 17713C>T missense_variant ORF1ab_pp1ab L5905F 9.25e-1 B.1.509
V4653 825G>T missense_variant ORF3a L275F 9.12e-1 B.1.509
V656 1981G>A missense_variant ORF1ab_pp1a G661S 1.00e+0 B.1.509
V6630 5547C>T synonymous_variant ORF1ab_pp1a D1849D 9.25e-1 B.1.509
V7941 15828C>T synonymous_variant ORF1ab_pp1ab Y5276Y 9.25e-1 B.1.509
V7959 15996C>T synonymous_variant ORF1ab_pp1ab C5332C 1.00e+0 B.1.509
V8036 16623C>T synonymous_variant ORF1ab_pp1ab Y5541Y 7.05e-1 B.1.509
V5416 532G>A missense_variant N G178S 7.07e-1 B.1.526
V4538 515G>A missense_variant ORF3a G172D 7.07e-1 B.1.560
V5347 214G>A missense_variant N V72I 7.07e-1 B.1.560
V7232 10278C>T synonymous_variant ORF1ab_pp1a H3426H 7.07e-1 B.1.560
V8053 16740C>T synonymous_variant ORF1ab_pp1ab L5580L 7.07e-1 B.1.560
V1109 3883G>T missense_variant ORF1ab_pp1a V1295F 7.07e-1 B.1.568
V2290 11854C>T missense_variant ORF1ab_pp1a P3952S 7.07e-1 B.1.568
V7269 10569C>T synonymous_variant ORF1ab_pp1a A3523A 7.07e-1 B.1.568
V7408 11740C>T synonymous_variant ORF1ab_pp1a L3914L 7.06e-1 B.1.568
V8056 16746C>T synonymous_variant ORF1ab_pp1ab I5582I 8.16e-1 B.1.568
V8592 20991G>T synonymous_variant ORF1ab_pp1ab A6997A 7.06e-1 B.1.568
V6425 4035G>T synonymous_variant ORF1ab_pp1a V1345V 1.00e+0 B.1.575
V4004 2008A>G missense_variant S I670V 1.00e+0 B.1.577
V1517 6386C>T missense_variant ORF1ab_pp1a A2129V 9.20e-1 B.1.596
V48 -92G>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 B.40
V5946 588C>T synonymous_variant ORF1ab_pp1a Y196Y 9.26e-1 B.40
V9590 126C>T synonymous_variant N P42P 8.66e-1 B.40
V2354 12407C>T missense_variant ORF1ab_pp1a A4136V 7.07e-1 B.6.6
V3808 916T>C missense_variant S F306L 1.00e+0 B.6.6
V3219 19254G>T missense_variant ORF1ab_pp1ab L6418F 7.07e-1 BA.1.1.14
V4710 -14C>T upstream_gene_variant M None 6.32e-1 BA.1.1.14
V5548 835C>T missense_variant N P279S 6.32e-1 BA.1.1.14
V4586 650C>T missense_variant ORF3a T217I 8.66e-1 BA.1.12
V2472 13353G>T missense_variant ORF1ab_pp1ab K4451N 7.07e-1 BA.1.20
V7179 9870T>A synonymous_variant ORF1ab_pp1a L3290L 7.07e-1 BA.2.10.1
V9776 1023C>T synonymous_variant N D341D 7.07e-1 BA.2.10.1
V4191 3310G>T missense_variant S V1104L 6.31e-1 BA.2.12
V9287 15C>T synonymous_variant M N5N 7.77e-1 BA.2.13
V2277 11788C>T missense_variant ORF1ab_pp1a L3930F 1.00e+0 BA.2.1
V1564 6619G>A missense_variant ORF1ab_pp1a G2207S 8.16e-1 BA.2.24
V4350 95C>T missense_variant ORF3a T32I 7.07e-1 BA.2.3.11
V8150 17442G>A synonymous_variant ORF1ab_pp1ab R5814R 1.00e+0 BA.2.3.13
V9129 3777C>T synonymous_variant S D1259D 1.00e+0 BA.2.3.13
V4398 160G>T missense_variant ORF3a A54S 1.00e+0 BA.2.3.7
V7084 9165C>T synonymous_variant ORF1ab_pp1a I3055I 1.00e+0 BA.2.38.2
V7523 12627G>A synonymous_variant ORF1ab_pp1a L4209L 7.07e-1 BA.2.38
V4198 3350C>T missense_variant S T1117I 1.00e+0 BA.2.40.1
V6339 3324C>T synonymous_variant ORF1ab_pp1a H1108H 1.00e+0 BA.2.40.1
V8144 17412C>T synonymous_variant ORF1ab_pp1ab I5804I 7.07e-1 BA.2.5
V7558 12936G>A synonymous_variant ORF1ab_pp1a P4312P 7.07e-1 BA.2.68
V8947 2478G>T synonymous_variant S V826V 1.00e+0 BA.2.75
V2437 13114G>A missense_variant ORF1ab_pp1a V4372I 7.07e-1 BA.4.1.8
V7093 9222C>T synonymous_variant ORF1ab_pp1a Y3074Y 8.82e-1 BA.4.6.5
V8445 19698G>A synonymous_variant ORF1ab_pp1ab T6566T 8.16e-1 BA.4.6.5
V9777 1038C>T synonymous_variant N F346F 7.38e-1 BA.5.1.17
V8688 414T>C synonymous_variant S D138D 8.82e-1 BA.5.1.1
V979 3322C>T missense_variant ORF1ab_pp1a H1108Y 7.78e-1 BA.5.1.1
V3376 20269A>G missense_variant ORF1ab_pp1ab I6757V 1.00e+0 BA.5.11
V2513 13598C>T missense_variant ORF1ab_pp1ab T4533I 1.00e+0 BA.5.1.27
V8292 18480C>T synonymous_variant ORF1ab_pp1ab Y6160Y 1.00e+0 BA.5.1.27
V7539 12765T>C synonymous_variant ORF1ab_pp1a G4255G 8.29e-1 BA.5.1.30
V5887 267A>G synonymous_variant ORF1ab_pp1a V89V 6.00e-1 BA.5.1.3
V6882 7593C>T synonymous_variant ORF1ab_pp1a N2531N 7.21e-1 BA.5.1.3
V205 274C>T missense_variant ORF1ab_pp1a L92F 1.00e+0 BA.5.2.34
V3585 212C>T missense_variant S S71F 1.00e+0 BA.5.2.34
V9737 876C>T synonymous_variant N I292I 1.00e+0 BA.5.3.1
V8592 20991G>T synonymous_variant ORF1ab_pp1ab A6997A 1.00e+0 BA.5.6.1
V845 2839T>C missense_variant ORF1ab_pp1a Y947H 8.94e-1 BA.5.6.2
V707 2204C>T missense_variant ORF1ab_pp1a A735V 7.70e-1 BA.5.9
V5735 *4322G>A downstream_gene_variant S None 6.62e-1 BF.10
V6047 1290C>T synonymous_variant ORF1ab_pp1a N430N 7.07e-1 BF.11
V101 -21C>T upstream_gene_variant ORF1ab_pp1a None 8.16e-1 BF.14
V6384 3747C>T synonymous_variant ORF1ab_pp1a L1249L 6.67e-1 BF.14
V9119 3714C>A synonymous_variant S T1238T 8.16e-1 BF.14
V4837 170C>T missense_variant ORF6 P57L 6.99e-1 BF.21
V8964 2568C>T synonymous_variant S N856N 7.82e-1 BF.21
V9369 483C>T synonymous_variant M I161I 8.39e-1 BF.21
V652 1967C>T missense_variant ORF1ab_pp1a A656V 1.00e+0 BF.3
V2563 13925C>T missense_variant ORF1ab_pp1ab A4642V 1.00e+0 BF.7.15
V4273 3711G>T missense_variant S M1237I 9.68e-1 BF.7.15
V5932 534C>T synonymous_variant ORF1ab_pp1a N178N 6.82e-1 BF.7.15
V7304 10908C>T synonymous_variant ORF1ab_pp1a L3636L 1.00e+0 BF.7.15
V8535 20559C>T synonymous_variant ORF1ab_pp1ab N6853N 6.82e-1 BF.7.15
V9318 243T>C synonymous_variant M A81A 1.00e+0 BF.7.15
V2339 12260C>T missense_variant ORF1ab_pp1a T4087I 7.37e-1 BF.7.6
V5653 1240G>T missense_variant N A414S 8.36e-1 BF.7.6
V6689 6021C>T synonymous_variant ORF1ab_pp1a T2007T 7.82e-1 BF.7.6
V7160 9720C>T synonymous_variant ORF1ab_pp1a D3240D 8.36e-1 BF.7.6
V5655 1247C>T missense_variant N S416L 1.00e+0 BF.7.8
V7384 11568C>T synonymous_variant ORF1ab_pp1a A3856A 8.66e-1 B
V2763 15929C>T missense_variant ORF1ab_pp1ab P5310L 7.07e-1 BL.1
V3104 18410G>A missense_variant ORF1ab_pp1ab R6137K 7.07e-1 BL.1
V6148 1998C>T synonymous_variant ORF1ab_pp1a T666T 1.00e+0 BL.1
V6386 3756C>T synonymous_variant ORF1ab_pp1a N1252N 1.00e+0 BL.1
V6428 4066C>T synonymous_variant ORF1ab_pp1a L1356L 1.00e+0 BL.1
V8303 18550C>T synonymous_variant ORF1ab_pp1ab L6184L 7.07e-1 BL.1
V1805 8372C>T missense_variant ORF1ab_pp1a T2791I 6.32e-1 BN.1.2
V2278 11801T>C missense_variant ORF1ab_pp1a M3934T 7.07e-1 BN.1.3
V7062 8958C>T synonymous_variant ORF1ab_pp1a H2986H 7.50e-1 BN.1.4
V8943 2460T>C synonymous_variant S D820D 7.07e-1 BN.1.4
V5932 534C>T synonymous_variant ORF1ab_pp1a N178N 7.07e-1 BQ.1.10
V1608 6854C>T missense_variant ORF1ab_pp1a S2285F 1.00e+0 BQ.1.1.10
V1840 8570T>C missense_variant ORF1ab_pp1a V2857A 1.00e+0 BQ.1.1.23
V1949 9413T>C missense_variant ORF1ab_pp1a F3138S 1.00e+0 BQ.1.1.23
V2185 11140G>A missense_variant ORF1ab_pp1a V3714I 1.00e+0 BQ.1.1.23
V2879 16879C>T missense_variant ORF1ab_pp1ab R5627C 1.00e+0 BQ.1.1.23
V2996 17765C>T missense_variant ORF1ab_pp1ab A5922V 1.00e+0 BQ.1.1.23
V4051 2168C>T missense_variant S T723I 1.00e+0 BQ.1.1.23
V5009 7G>A missense_variant ORF7b E3K 1.00e+0 BQ.1.1.23
V566 1657G>A missense_variant ORF1ab_pp1a E553K 1.00e+0 BQ.1.1.23
V817 2732C>T missense_variant ORF1ab_pp1a S911F 7.07e-1 BQ.1.1.23
V9487 360A>G synonymous_variant ORF7a T120T 1.00e+0 BQ.1.1.23
V9655 474G>A synonymous_variant N V158V 7.07e-1 BQ.1.1.23
V9715 777G>A synonymous_variant N R259R 1.00e+0 BQ.1.1.23
V4513 418C>T missense_variant ORF3a L140F 1.00e+0 BQ.1.1.29
V2227 11326C>T missense_variant ORF1ab_pp1a L3776F 6.12e-1 BQ.1.12
V1354 5621C>T missense_variant ORF1ab_pp1a T1874I 1.00e+0 BQ.1.13.1
V3154 18745G>T missense_variant ORF1ab_pp1ab D6249Y 1.00e+0 BQ.1.13.1
V1340 5519C>T missense_variant ORF1ab_pp1a T1840I 1.00e+0 BY.1
V1971 9605C>T missense_variant ORF1ab_pp1a T3202M 1.00e+0 BY.1
V4500 379C>T missense_variant ORF3a L127F 1.00e+0 BY.1
V5721 *4295C>T downstream_gene_variant S None 7.07e-1 BY.1
V6200 2358C>T synonymous_variant ORF1ab_pp1a N786N 7.07e-1 BY.1
V6817 7002C>T synonymous_variant ORF1ab_pp1a F2334F 7.07e-1 BY.1
V7132 9571C>T synonymous_variant ORF1ab_pp1a L3191L 1.00e+0 BY.1
V7230 10260C>T synonymous_variant ORF1ab_pp1a V3420V 1.00e+0 BY.1
V7467 12147C>T synonymous_variant ORF1ab_pp1a I4049I 1.00e+0 BY.1
V5432 560C>T missense_variant N S187L 1.00e+0 C.36
V6106 1732C>T synonymous_variant ORF1ab_pp1a L578L 8.16e-1 CJ.1
V6777 6703C>T synonymous_variant ORF1ab_pp1a L2235L 7.07e-1 CJ.1
V7352 11385C>T synonymous_variant ORF1ab_pp1a G3795G 8.16e-1 CJ.1
V9665 519A>T synonymous_variant N A173A 7.07e-1 CJ.1
V1951 9428C>T missense_variant ORF1ab_pp1a A3143V 1.00e+0 DL.1
V9325 300C>T synonymous_variant M F100F 8.16e-1 DL.1
V2184 11136G>T missense_variant ORF1ab_pp1a M3712I 7.96e-1 P.1.2
V4410 175G>T missense_variant ORF3a A59S 7.05e-1 P.1.2
V4466 298G>T missense_variant ORF3a G100C 8.36e-1 P.1.2
V4965 277G>T missense_variant ORF7a V93F 7.62e-1 P.1.2
V6123 1845C>T synonymous_variant ORF1ab_pp1a N615N 7.32e-1 P.1.2
V6217 2436C>T synonymous_variant ORF1ab_pp1a T812T 7.62e-1 P.1.2
V6507 4662C>T synonymous_variant ORF1ab_pp1a D1554D 7.62e-1 P.1.2
V6818 7014C>T synonymous_variant ORF1ab_pp1a F2338F 6.04e-1 P.1.2
V6977 8340C>T synonymous_variant ORF1ab_pp1a F2780F 6.66e-1 P.1.2
V7390 11619C>T synonymous_variant ORF1ab_pp1a L3873L 8.36e-1 P.1.2
V8913 2187G>T synonymous_variant S V729V 7.07e-1 P.2
V991 3373G>A missense_variant ORF1ab_pp1a G1125S 7.07e-1 P.2
V4730 67G>T missense_variant M V23L 7.07e-1 XBB.2
V5544 812C>T missense_variant N T271I 7.55e-1 XBB
V8547 20667G>T synonymous_variant ORF1ab_pp1ab T6889T 9.26e-1 XBB
V4569 584C>T missense_variant ORF3a S195F 1.00e+0 B.1.1.186
V6939 8025C>T synonymous_variant ORF1ab_pp1a L2675L 1.00e+0 B.1.1.186
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 8.60e-1 B.1.1.205
V9508 27C>T synonymous_variant ORF8 I9I 8.60e-1 B.1.1.205
V3081 18247C>T missense_variant ORF1ab_pp1ab P6083S 7.06e-1 B.1.1.231
V3239 19413G>T missense_variant ORF1ab_pp1ab Q6471H 1.00e+0 B.1.1.274
V5683 10A>C missense_variant ORF10 I4L 1.00e+0 B.1.1.274
V5814 *4395G>T downstream_gene_variant S None 1.00e+0 B.1.1.274
V5943 576C>T synonymous_variant ORF1ab_pp1a G192G 7.06e-1 B.1.1.274
V8787 1233T>C synonymous_variant S A411A 1.00e+0 B.1.1.274
V4079 2386G>T missense_variant S D796Y 6.96e-1 B.1.1.346
V4210 3415G>C missense_variant S D1139H 1.00e+0 B.1.1.346
V2638 14593G>T missense_variant ORF1ab_pp1ab V4865F 1.00e+0 B.1.1.397
V5759 *4349C>T downstream_gene_variant S None 1.00e+0 B.1.1.397
V5807 *4385C>T downstream_gene_variant S None 1.00e+0 B.1.1.397
V6546 4927C>T synonymous_variant ORF1ab_pp1a L1643L 1.00e+0 B.1.1.397
V7572 12990C>T synonymous_variant ORF1ab_pp1a C4330C 1.00e+0 B.1.1.397
V5959 666T>C synonymous_variant ORF1ab_pp1a I222I 1.00e+0 B.1.1.485
V7998 16290T>C synonymous_variant ORF1ab_pp1ab F5430F 1.00e+0 B.1.1.485
V8584 20955C>T synonymous_variant ORF1ab_pp1ab F6985F 1.00e+0 B.1.1.485
V9389 609C>T synonymous_variant M N203N 7.00e-1 B.1.1.485
V964 3277A>G missense_variant ORF1ab_pp1a T1093A 1.00e+0 B.1.1.485
V1112 3915G>T missense_variant ORF1ab_pp1a K1305N -7.61e-1 B.1.221.4
V5263 27G>T missense_variant N Q9H 6.69e-1 B.1.221.4
V5441 578G>T missense_variant N S193I 7.61e-1 B.1.221.4
V562 1649G>A missense_variant ORF1ab_pp1a R550H -7.61e-1 B.1.221.4
V6182 2220C>T synonymous_variant ORF1ab_pp1a I740I -7.61e-1 B.1.221.4
V7427 11850C>T synonymous_variant ORF1ab_pp1a S3950S -7.27e-1 B.1.221.4
V7745 14340A>G synonymous_variant ORF1ab_pp1ab L4780L -7.61e-1 B.1.221.4
V79 -48C>T upstream_gene_variant ORF1ab_pp1a None -6.55e-1 B.1.221.4
V1183 4529C>T missense_variant ORF1ab_pp1a S1510F 1.00e+0 B.1.248
V4312 37G>T missense_variant ORF3a V13L -1.00e+0 B.1.248
V4613 751G>A missense_variant ORF3a G251S 1.00e+0 B.1.248
V7069 9021C>T synonymous_variant ORF1ab_pp1a N3007N 1.00e+0 B.1.248
V7397 11676C>T synonymous_variant ORF1ab_pp1a V3892V 1.00e+0 B.1.248
V7704 14058C>T synonymous_variant ORF1ab_pp1ab Y4686Y 1.00e+0 B.1.248
V8407 19338C>T synonymous_variant ORF1ab_pp1ab N6446N 6.97e-1 B.1.248
V8436 19620C>T synonymous_variant ORF1ab_pp1ab Y6540Y 1.00e+0 B.1.248
V8604 21093T>C synonymous_variant ORF1ab_pp1ab N7031N 1.00e+0 B.1.248
V3239 19413G>T missense_variant ORF1ab_pp1ab Q6471H 8.13e-1 B.1.256
V5943 576C>T synonymous_variant ORF1ab_pp1a G192G 8.13e-1 B.1.256
V8787 1233T>C synonymous_variant S A411A 7.68e-1 B.1.256
V1096 3814A>G missense_variant ORF1ab_pp1a S1272G 1.00e+0 B.1.36.38
V149 136C>T missense_variant ORF1ab_pp1a L46F 1.00e+0 B.1.36.38
V8154 17469C>T synonymous_variant ORF1ab_pp1ab F5823F 7.06e-1 B.1.36.38
V9207 435T>C synonymous_variant ORF3a Y145Y 7.06e-1 B.1.36.38
V9521 108G>A synonymous_variant ORF8 P36P 7.06e-1 B.1.36.38
V4692 212C>T missense_variant E P71L 7.06e-1 B.1.384
V5275 40C>T missense_variant N R14C 7.06e-1 B.1.384
V8624 33C>T synonymous_variant S V11V 1.00e+0 B.1.384
V3920 1468T>G missense_variant S F490V 1.00e+0 B.1.390
V1452 6167C>T missense_variant ORF1ab_pp1a T2056I 1.00e+0 B.1.441
V2852 16738C>T missense_variant ORF1ab_pp1ab L5580F 7.04e-1 B.1.441
V3484 21040C>A missense_variant ORF1ab_pp1ab R7014S 1.00e+0 B.1.441
V4454 280C>T missense_variant ORF3a L94F 1.00e+0 B.1.441
V6656 5772C>T synonymous_variant ORF1ab_pp1a S1924S 1.00e+0 B.1.441
V7209 10104C>T synonymous_variant ORF1ab_pp1a R3368R 7.04e-1 B.1.441
V9407 96C>T synonymous_variant ORF6 I32I 1.00e+0 B.1.441
V1574 6725C>T missense_variant ORF1ab_pp1a S2242F 7.05e-1 B.1.468
V4535 512C>T missense_variant ORF3a S171L 1.00e+0 B.1.468
V4681 151C>T missense_variant E L51F 1.00e+0 B.1.468
V8515 20364C>T synonymous_variant ORF1ab_pp1ab G6788G 7.05e-1 B.1.468
V482 1328C>T missense_variant ORF1ab_pp1a S443F 7.04e-1 B.1.478
V7197 9963C>T synonymous_variant ORF1ab_pp1a L3321L 1.00e+0 B.1.478
V8056 16746C>T synonymous_variant ORF1ab_pp1ab I5582I 1.00e+0 B.1.478
V4015 2031G>T missense_variant S Q677H 8.61e-1 B.1.540
V4100 2533G>T missense_variant S A845S 1.00e+0 B.1.540
V758 2411C>T missense_variant ORF1ab_pp1a P804L 6.98e-1 B.1.540
V886 2986G>A missense_variant ORF1ab_pp1a D996N 1.00e+0 B.1.540
V9330 312G>T synonymous_variant M A104A 6.98e-1 B.1.540
V2207 11249C>T missense_variant ORF1ab_pp1a T3750I 8.12e-1 B.1.543
V3604 268G>A missense_variant S V90I 8.12e-1 B.1.543
V4433 221C>T missense_variant ORF3a S74F 8.12e-1 B.1.543
V4531 494C>T missense_variant ORF3a S165F 1.00e+0 B.1.543
V7544 12807C>T synonymous_variant ORF1ab_pp1a F4269F 8.12e-1 B.1.543
V8626 60C>T synonymous_variant S T20T 8.61e-1 B.1.543
V8751 918C>T synonymous_variant S F306F 1.00e+0 B.1.543
V8789 1239G>A synonymous_variant S G413G 1.00e+0 B.1.543
V9224 618C>T synonymous_variant ORF3a Y206Y 8.12e-1 B.1.543
V1782 8234C>T missense_variant ORF1ab_pp1a A2745V 6.55e-1 B.1.614
V8973 2637G>T synonymous_variant S A879A 6.55e-1 B.1.614
V5051 122G>C missense_variant ORF7b C41S 1.00e+0 B.1.634
V6052 1329C>T synonymous_variant ORF1ab_pp1a S443S 7.06e-1 B.1.634
V8601 21042C>T synonymous_variant ORF1ab_pp1ab R7014R 8.12e-1 B.1.639
V4613 751G>A missense_variant ORF3a G251S 1.00e+0 B.1.78
V6226 2499G>T synonymous_variant ORF1ab_pp1a V833V 1.00e+0 B.1.78
V6923 7887C>T synonymous_variant ORF1ab_pp1a V2629V 1.00e+0 B.1.78
V7704 14058C>T synonymous_variant ORF1ab_pp1ab Y4686Y 1.00e+0 B.1.78
V7741 14310T>C synonymous_variant ORF1ab_pp1ab P4770P 1.00e+0 B.1.78
V9233 666C>T synonymous_variant ORF3a D222D 1.00e+0 B.1.78
V1511 6368C>T missense_variant ORF1ab_pp1a A2123V 1.00e+0 BQ.1.1.30
V2350 12358C>T missense_variant ORF1ab_pp1a P4120S 1.00e+0 BQ.1.1.30
V4669 61C>T missense_variant E L21F 1.00e+0 BQ.1.1.30
V9323 279C>T synonymous_variant M L93L 1.00e+0 BQ.1.1.30
V2183 11131C>T missense_variant ORF1ab_pp1a L3711F 1.00e+0 C.4
V1839 8567C>T missense_variant ORF1ab_pp1a A2856V 1.00e+0 CG.1
V3889 1379A>G missense_variant S N460S 1.00e+0 CG.1
V4218 3440C>T missense_variant S S1147L 9.10e-1 CK.2
V5461 608G>A missense_variant N R203K -6.91e-1 CK.2
V5465 610G>C missense_variant N G204R -6.91e-1 CK.2
V8397 19272C>T synonymous_variant ORF1ab_pp1ab N6424N 8.73e-1 CK.2
V9682 609G>A synonymous_variant N R203R -6.91e-1 CK.2





Manual curation of mutation (7125C>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