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The current mutation

ID: V2267
DNA: 11743C>T
Protein: L3915F
Position: 12008








COV2Var annotation categories







Summary information of mutation (11743C>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   12008
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 11743C>T
  Ref Seq: C
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: L3915F
  Protein 3-letter Mutation: Leu3915Phe

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 (11743C>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.1.1.47 43 10 2.33e-1
2020-10 B.1.1 43 8 1.86e-1
2020-10 B.1.1.500 43 4 9.30e-2
2020-11 B.1.177.57 30 6 2.00e-1
2020-11 B.1.1.500 30 4 1.33e-1
2020-11 B.1.396 30 4 1.33e-1
2020-12 B.1.243 35 8 2.29e-1
2020-12 B.1.1.7 35 6 1.71e-1
2020-12 B.1.1 35 3 8.57e-2
2020-03 B 4 1 2.50e-1
2020-03 B.1 4 1 2.50e-1
2020-03 B.1.1 4 1 2.50e-1
2020-04 B.1 5 2 4.00e-1
2020-04 B.1.413 5 2 4.00e-1
2020-04 B.1.1 5 1 2.00e-1
2020-05 B.1.1 7 3 4.29e-1
2020-05 B.1 7 2 2.86e-1
2020-05 B.1.221 7 1 1.43e-1
2020-06 B.1.1.1 13 4 3.08e-1
2020-06 B.1.1.500 13 4 3.08e-1
2020-06 B.1 13 2 1.54e-1
2020-07 B.1.1 12 8 6.67e-1
2020-07 B.1.1.398 12 2 1.67e-1
2020-07 B.1.234 12 1 8.33e-2
2020-08 B.1.1.500 14 6 4.29e-1
2020-08 B.1.1 14 2 1.43e-1
2020-08 B.1.1.222 14 2 1.43e-1
2020-09 B.1.1.464 18 6 3.33e-1
2020-09 B.1.1.317 18 5 2.78e-1
2020-09 B.1.1 18 3 1.67e-1
2021-01 B.1.1.7 87 29 3.33e-1
2021-01 B.1.243 87 9 1.03e-1
2021-01 B.1.427 87 7 8.05e-2
2021-10 AY.5 666 379 5.69e-1
2021-10 AY.9.2 666 104 1.56e-1
2021-10 AY.25.1 666 59 8.86e-2
2021-11 AY.5 659 252 3.82e-1
2021-11 AY.9.2 659 160 2.43e-1
2021-11 AY.25.1 659 59 8.95e-2
2021-12 AY.9.2 431 103 2.39e-1
2021-12 AY.5 431 101 2.34e-1
2021-12 AY.25.1 431 70 1.62e-1
2021-02 B.1.1.7 147 41 2.79e-1
2021-02 B.1.351 147 32 2.18e-1
2021-02 B.1.243 147 14 9.52e-2
2021-03 B.1.1.7 487 228 4.68e-1
2021-03 B.1.351 487 123 2.53e-1
2021-03 P.4 487 53 1.09e-1
2021-04 B.1.1.7 442 201 4.55e-1
2021-04 B.1.351 442 94 2.13e-1
2021-04 P.4 442 80 1.81e-1
2021-05 B.1.1.7 350 145 4.14e-1
2021-05 B.1.351 350 94 2.69e-1
2021-05 P.4 350 63 1.80e-1
2021-06 B.1.351 430 289 6.72e-1
2021-06 P.4 430 54 1.26e-1
2021-06 B.1.1.7 430 42 9.77e-2
2021-07 AY.5 2292 1978 8.63e-1
2021-07 B.1.351 2292 234 1.02e-1
2021-07 AY.4 2292 20 8.73e-3
2021-08 AY.5 1866 1580 8.47e-1
2021-08 AY.9.2 1866 105 5.63e-2
2021-08 B.1.351 1866 48 2.57e-2
2021-09 AY.5 989 774 7.83e-1
2021-09 AY.9.2 989 79 7.99e-2
2021-09 AY.4 989 15 1.52e-2
2022-01 BA.1.1 234 63 2.69e-1
2022-01 BA.2 234 55 2.35e-1
2022-01 BA.1 234 21 8.97e-2
2022-10 BE.1.1.2 156 66 4.23e-1
2022-10 BF.10 156 37 2.37e-1
2022-10 BA.5.6 156 9 5.77e-2
2022-11 BF.10 83 19 2.29e-1
2022-11 BA.5.6 83 5 6.02e-2
2022-11 BF.14 83 5 6.02e-2
2022-12 BF.14 90 13 1.44e-1
2022-12 BQ.1.1 90 13 1.44e-1
2022-12 BF.10 90 8 8.89e-2
2022-02 BA.2 671 527 7.85e-1
2022-02 BA.1.1 671 66 9.84e-2
2022-02 BA.1 671 17 2.53e-2
2022-03 BA.2 1253 1142 9.11e-1
2022-03 BA.2.9 1253 30 2.39e-2
2022-03 BA.1.1 1253 23 1.84e-2
2022-04 BA.2 545 452 8.29e-1
2022-04 BA.2.9 545 42 7.71e-2
2022-04 BA.2.3 545 16 2.94e-2
2022-05 BA.2 354 268 7.57e-1
2022-05 BA.2.3 354 30 8.47e-2
2022-05 BA.2.10 354 13 3.67e-2
2022-06 BA.2 165 104 6.30e-1
2022-06 BA.4.1 165 20 1.21e-1
2022-06 BA.5.5 165 5 3.03e-2
2022-07 BA.4.1 130 44 3.38e-1
2022-07 BA.2 130 31 2.38e-1
2022-07 BA.5.5 130 10 7.69e-2
2022-08 BE.1.1.2 123 32 2.60e-1
2022-08 BA.4.1 123 28 2.28e-1
2022-08 BA.2 123 8 6.50e-2
2022-09 BE.1.1.2 158 66 4.18e-1
2022-09 BA.4.6 158 16 1.01e-1
2022-09 BF.26 158 12 7.59e-2
2023-01 BF.7.5 89 14 1.57e-1
2023-01 XBB.1.5 89 12 1.35e-1
2023-01 BQ.1.1 89 10 1.12e-1
2023-02 XBB.1.5 47 14 2.98e-1
2023-02 CH.1.1.3 47 5 1.06e-1
2023-02 BF.7.5 47 4 8.51e-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
V2267 AY.5 8.26e-2 5093 2020-9-8 2022-7-26
V2267 AY.62 1.95e-2 43 2021-4-20 2022-8-12
V2267 AY.80 2.67e-2 33 2021-6-2 2022-1-8
V2267 AY.9.2 1.16e-2 567 2020-10-15 2022-5-26
V2267 B.1.1.47 2.99e-2 5 2020-7-1 2021-12-10
V2267 B.1.1.500 2.77e-1 13 2020-4-10 2021-3-2
V2267 B.1.351 2.95e-2 921 2020-2-18 2022-10-26
V2267 B.1.367 1.20e-2 11 2020-7-13 2021-12-7
V2267 B.1.639 6.48e-1 35 2021-1-19 2021-11-15
V2267 BE.1.1.2 2.42e-2 166 2022-4-7 2023-1-30
V2267 CH.1 1.07e-2 3 2022-8-17 2023-2-20
V2267 P.4 9.96e-1 270 2021-2-17 2021-9-9






Examining mutation (11743C>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
Neovison vison B.1.1.298 Denmark 2020-10-16 EPI_ISL_683280
Odocoileus virginianus AY.103 USA 2021-11-30 EPI_ISL_16308765
Odocoileus virginianus AY.113 USA 2021-11-21 EPI_ISL_16297218
Odocoileus virginianus B.1.617.2 USA 2021-11-21 EPI_ISL_16297245
Neovison vison AY.5 Latvia 2021-11-23 EPI_ISL_10217387




Association between mutation (11743C>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 -1.32e+0 3.70e-1 -3.56e+0 3.75e-4 Decrease
Deceased -8.54e-1 2.70e-1 -3.16e+0 1.58e-3 Decrease
Homebound -1.61e+1 1.77e+3 -9.06e-3 9.93e-1 Decrease
Hospitalized -1.34e+0 1.81e-1 -7.40e+0 1.40e-13 Decrease
Mild -1.56e+1 3.91e+2 -3.98e-2 9.68e-1 Decrease
Recovered 1.05e+0 1.54e-1 6.77e+0 1.30e-11 Increase

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 2.19e-3 6.15e-2 3.56e-2 9.72e-1 Increase
18-39 5.16e-1 3.44e-2 1.50e+1 5.82e-51 Increase
40-64 -3.04e-1 3.78e-2 -8.04e+0 8.99e-16 Decrease
65-84 -3.92e-1 5.75e-2 -6.81e+0 9.63e-12 Decrease
>=85 -8.01e-1 1.32e-1 -6.07e+0 1.26e-9 Decrease

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

Attribute Effect Estimate SE Z-value P-value Direction
Patient gender Male -3.30e-2 3.43e-2 -9.60e-1 3.37e-1 Decrease





Investigating natural selection at mutation (11743C>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
nsp7 11843 12091 83 56 12.46 1.44 4.00e-2 BA.5.2.27 FEL
nsp7 11843 12091 83 56 0.00 6.02 4.00e-2 AY.5 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
nsp7 11843 12091 83 56 9.90e-1 0.00e+0 BA.5.2.27 FUBAR
nsp7 11843 12091 83 56 0.00e+0 9.90e-1 AY.5 FUBAR




Alterations in protein physicochemical properties induced by mutation (11743C>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_pp1a 490022.93 6.04 543550 88.9 -0.024
Reference ORF1ab_pp1a 489988.91 6.04 543550 88.99 -0.023




Alterations in protein stability induced by mutation (11743C>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
L3915F ORF1ab_pp1a Point 3915 0.11 Increase 7 25 Environment
L3915F ORF1ab_pp1a Point 3915 0.09 Increase 7.4 37 Internal




Impact on protein function induced by mutation (11743C>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
L3915F ORF1ab_pp1a Point 0.293 Altered Coiled_coil (Pr = 0.04 | P = 0.07)




Exploring mutation (11743C>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 (11743C>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
L3915F ORF1ab_pp1a 12008 Chymotrypsin-high specificity VSLFSVLLSM (pos: 3915)
 NA




Impact of spike protein mutation (11743C>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 (11743C>T) on viral transmissibility by the affinity between RBD and ACE2 receptor

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

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


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

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        Show interface residues:





Impact of mutation (11743C>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 (11743C>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
V4446 262G>T missense_variant ORF3a V88L 8.35e-1 AY.5
V5742 *4327G>T downstream_gene_variant S None 8.20e-1 AY.5
V2583 14030G>A missense_variant ORF1ab_pp1ab R4677H 7.07e-1 BE.1.1
V7530 12699A>G synonymous_variant ORF1ab_pp1a G4233G 7.17e-1 BE.1.1
V5742 *4327G>T downstream_gene_variant S None 8.81e-1 AY.9.2
V8000 16308T>C synonymous_variant ORF1ab_pp1ab C5436C 6.32e-1 AY.98
V8123 17206C>T synonymous_variant ORF1ab_pp1ab L5736L 6.39e-1 AY.98
V5947 597G>A synonymous_variant ORF1ab_pp1a E199E 7.59e-1 BA.1.15.1
V3143 18695C>T missense_variant ORF1ab_pp1ab A6232V 8.16e-1 AY.101
V8982 2757C>T synonymous_variant S N919N 7.07e-1 AY.102
V4497 375G>T missense_variant ORF3a M125I 1.00e+0 AY.10
V471 1293A>G missense_variant ORF1ab_pp1a I431M 1.00e+0 AY.10
V2679 15088C>T missense_variant ORF1ab_pp1ab L5030F 1.00e+0 AY.110
V5504 655C>T missense_variant N L219F 1.00e+0 AY.110
V6835 7164A>G synonymous_variant ORF1ab_pp1a A2388A 1.00e+0 AY.110
V7570 12984G>T synonymous_variant ORF1ab_pp1a L4328L 1.00e+0 AY.110
V4446 262G>T missense_variant ORF3a V88L 7.07e-1 AY.111
V5742 *4327G>T downstream_gene_variant S None 7.07e-1 AY.111
V5789 *4367G>C downstream_gene_variant S None 1.00e+0 AY.111
V5198 308C>T missense_variant ORF8 S103L 7.07e-1 AY.113
V2873 16858G>T missense_variant ORF1ab_pp1ab A5620S 7.69e-1 AY.116
V5139 175G>T stop_gained ORF8 E59* 9.43e-1 AY.116
V5271 35C>T missense_variant N A12V 9.43e-1 AY.116
V7776 14517T>C synonymous_variant ORF1ab_pp1ab N4839N 9.43e-1 AY.116
V9199 339C>T synonymous_variant ORF3a Y113Y 8.43e-1 AY.116
V8295 18492G>A synonymous_variant ORF1ab_pp1ab P6164P 1.00e+0 AY.119.1
V9560 9T>C synonymous_variant N D3D 7.07e-1 AY.119.1
V2542 13777A>G missense_variant ORF1ab_pp1ab I4593V 7.07e-1 AY.124
V9533 195T>A synonymous_variant ORF8 A65A 7.07e-1 AY.124
V2405 12746C>T missense_variant ORF1ab_pp1a T4249I 7.07e-1 AY.13
V3608 284C>T missense_variant S T95I 7.07e-1 AY.17
V3894 1424C>T missense_variant S A475V 1.00e+0 AY.17
V3924 1480T>C missense_variant S S494P 1.00e+0 AY.17
V3928 1502A>C missense_variant S N501T 1.00e+0 AY.17
V3997 1963C>T missense_variant S H655Y 1.00e+0 AY.17
V4111 2576C>A missense_variant S T859N 1.00e+0 AY.17
V4536 514G>C missense_variant ORF3a G172R 1.00e+0 AY.17
V5274 38C>T missense_variant N P13L 1.00e+0 AY.17
V702 2188C>T missense_variant ORF1ab_pp1a L730F 8.16e-1 AY.17
V7682 13914C>T synonymous_variant ORF1ab_pp1ab T4638T 7.06e-1 AY.17
V804 2672C>T missense_variant ORF1ab_pp1a T891I 1.00e+0 AY.17
V8204 17856C>T synonymous_variant ORF1ab_pp1ab L5952L 1.00e+0 AY.17
V9677 576C>T synonymous_variant N N192N 1.00e+0 AY.17
V9707 747A>G synonymous_variant N K249K 1.00e+0 AY.17
V6623 5466T>G synonymous_variant ORF1ab_pp1a T1822T 7.07e-1 AY.23
V8889 2004A>T synonymous_variant S A668A 7.07e-1 AY.23
V3632 423G>T missense_variant S L141F 7.07e-1 AY.24
V4833 158A>G missense_variant ORF6 D53G 1.00e+0 AY.24
V2767 15958C>T missense_variant ORF1ab_pp1ab H5320Y 1.00e+0 AY.29.2
V5115 113C>T missense_variant ORF8 P38L 1.00e+0 AY.29.2
V3153 18745G>A missense_variant ORF1ab_pp1ab D6249N 1.00e+0 AY.3.1
V2262 11679G>T missense_variant ORF1ab_pp1a Q3893H 8.45e-1 AY.33
V8418 19491T>C synonymous_variant ORF1ab_pp1ab N6497N 6.20e-1 AY.33
V6055 1347C>T synonymous_variant ORF1ab_pp1a N449N 1.00e+0 AY.36
V1391 5855C>T missense_variant ORF1ab_pp1a S1952L 7.07e-1 AY.39.1
V1340 5519C>T missense_variant ORF1ab_pp1a T1840I 7.74e-1 AY.4.11
V178 245_250delGTCATG disruptive_inframe_deletion ORF1ab_pp1a G82_H83del 1.00e+0 AY.4.11
V6496 4611C>T synonymous_variant ORF1ab_pp1a Y1537Y 1.00e+0 AY.4.11
V8090 16983T>C synonymous_variant ORF1ab_pp1ab R5661R 1.00e+0 AY.4.11
V990 3369C>A missense_variant ORF1ab_pp1a N1123K 1.00e+0 AY.4.11
V230 340A>G missense_variant ORF1ab_pp1a I114V 1.00e+0 AY.4.12
V5858 117A>G synonymous_variant ORF1ab_pp1a L39L 1.00e+0 AY.4.13
V2171 11034G>T missense_variant ORF1ab_pp1a K3678N 7.07e-1 AY.4.5
V5046 115G>C missense_variant ORF7b E39Q 7.07e-1 AY.4.5
V4883 100C>T missense_variant ORF7a P34S 1.00e+0 AY.46.1
V7001 8553C>T synonymous_variant ORF1ab_pp1a C2851C 1.00e+0 AY.51
V428 1127C>T missense_variant ORF1ab_pp1a S376L 7.07e-1 AY.5.3
V4446 262G>T missense_variant ORF3a V88L 8.66e-1 AY.5.3
V4900 134C>T missense_variant ORF7a P45L 7.07e-1 AY.5.3
V5742 *4327G>T downstream_gene_variant S None 6.70e-1 AY.5.3
V3173 18854C>T missense_variant ORF1ab_pp1ab A6285V 1.00e+0 AY.53
V344 802G>A missense_variant ORF1ab_pp1a G268R 1.00e+0 AY.53
V6485 4512C>T synonymous_variant ORF1ab_pp1a T1504T 7.07e-1 AY.53
V4446 262G>T missense_variant ORF3a V88L 1.00e+0 AY.5.4
V5742 *4327G>T downstream_gene_variant S None 7.25e-1 AY.5.4
V1594 6793G>A missense_variant ORF1ab_pp1a G2265S 7.07e-1 AY.54
V4521 452C>T missense_variant ORF3a T151I 7.07e-1 AY.5.5
V5281 53G>T missense_variant N G18V 7.07e-1 AY.5.5
V5742 *4327G>T downstream_gene_variant S None 7.07e-1 AY.5.5
V6362 3522C>T synonymous_variant ORF1ab_pp1a Y1174Y 7.07e-1 AY.5.5
V6461 4317C>T synonymous_variant ORF1ab_pp1a N1439N 7.07e-1 AY.5.5
V9582 105G>T synonymous_variant N A35A 7.07e-1 AY.5.5
V1029 3525A>T missense_variant ORF1ab_pp1a L1175F 8.90e-1 AY.62
V5884 262C>T synonymous_variant ORF1ab_pp1a L88L 1.00e+0 AY.62
V7685 13923G>A synonymous_variant ORF1ab_pp1ab R4641R 7.71e-1 AY.75
V4758 241G>T missense_variant M A81S 8.16e-1 AY.78
V609 1802T>C missense_variant ORF1ab_pp1a I601T 1.00e+0 AY.78
V7019 8652C>T synonymous_variant ORF1ab_pp1a F2884F 1.00e+0 AY.78
V8412 19398C>T synonymous_variant ORF1ab_pp1ab H6466H 8.16e-1 AY.78
V2614 14323G>T missense_variant ORF1ab_pp1ab A4775S 7.65e-1 AY.80
V6352 3423C>T synonymous_variant ORF1ab_pp1a H1141H 1.00e+0 AY.85
V5205 334C>T missense_variant ORF8 H112Y 1.00e+0 AY.93
V129 82G>A missense_variant ORF1ab_pp1a V28I 7.07e-1 AY.99.1
V2494 13484A>G missense_variant ORF1ab_pp1ab K4495R 7.07e-1 AY.99.1
V2645 14738A>G missense_variant ORF1ab_pp1ab Y4913C 7.07e-1 AY.99.1
V2814 16462C>T missense_variant ORF1ab_pp1ab H5488Y 7.07e-1 AY.99.1
V3598 238G>T missense_variant S D80Y 7.07e-1 AY.99.1
V4154 3058G>T missense_variant S A1020S 7.07e-1 AY.99.1
V5684 10A>G missense_variant ORF10 I4V 7.07e-1 AY.99.1
V7459 12063G>A synonymous_variant ORF1ab_pp1a K4021K 7.07e-1 AY.99.1
V7677 13854G>T synonymous_variant ORF1ab_pp1ab T4618T 7.07e-1 AY.99.1
V8451 19752C>T synonymous_variant ORF1ab_pp1ab D6584D 7.07e-1 AY.99.1
V8640 159C>T synonymous_variant S D53D 7.07e-1 AY.99.1
V8915 2196C>T synonymous_variant S T732T 7.07e-1 AY.99.1
V1794 8330C>T missense_variant ORF1ab_pp1a T2777I 1.00e+0 AY.99.2
V1443 6139G>T missense_variant ORF1ab_pp1a V2047F 7.74e-1 B.1.1.1
V6655 5766C>T synonymous_variant ORF1ab_pp1a N1922N 6.70e-1 B.1.1.1
V9827 57C>T synonymous_variant ORF10 C19C 6.32e-1 B.1.1.1
V1329 5441A>G missense_variant ORF1ab_pp1a Y1814C 1.00e+0 B.1.1.216
V1340 5519C>T missense_variant ORF1ab_pp1a T1840I 7.07e-1 B.1.1.222
V161 178G>A missense_variant ORF1ab_pp1a V60I 7.07e-1 B.1.1.263
V5543 808G>T missense_variant N V270L 7.07e-1 B.1.1.263
V6900 7752G>T synonymous_variant ORF1ab_pp1a A2584A 7.07e-1 B.1.1.298
V1340 5519C>T missense_variant ORF1ab_pp1a T1840I 1.00e+0 B.1.1.306
V2434 13091C>T missense_variant ORF1ab_pp1a T4364I 1.00e+0 B.1.1.306
V4112 2576C>T missense_variant S T859I 8.95e-1 B.1.1.317
V1369 5761C>T missense_variant ORF1ab_pp1a P1921S 7.07e-1 B.1.1.372
V5559 898C>T missense_variant N H300Y 1.00e+0 B.1.1.372
V7610 13272C>T synonymous_variant ORF1ab_pp1ab Y4424Y 1.00e+0 B.1.1.523
V8644 174C>T synonymous_variant S F58F 6.31e-1 B.1.1.523
V5706 70C>T missense_variant ORF10 R24C 8.16e-1 B.1.1.63
V8260 18222C>T synonymous_variant ORF1ab_pp1ab L6074L 6.11e-1 B.1.1.63
V1281 5061G>T missense_variant ORF1ab_pp1a E1687D 7.07e-1 B.1.177.45
V1909 9083C>T missense_variant ORF1ab_pp1a T3028I 1.00e+0 B.1.177.45
V4319 52G>T missense_variant ORF3a G18C 1.00e+0 B.1.177.57
V4321 53G>T missense_variant ORF3a G18V 9.26e-1 B.1.177.57
V7684 13920C>T synonymous_variant ORF1ab_pp1ab T4640T 9.26e-1 B.1.177.57
V8113 17163G>T synonymous_variant ORF1ab_pp1ab V5721V 1.00e+0 B.1.177.57
V1021 3478C>T missense_variant ORF1ab_pp1a H1160Y 7.07e-1 B.1.177.60
V2827 16579G>T missense_variant ORF1ab_pp1ab G5527C 1.00e+0 B.1.177.60
V9288 27C>T synonymous_variant M T9T 7.07e-1 B.1.177.60
V4884 101C>T missense_variant ORF7a P34L 1.00e+0 B.1.177.73
V8712 633T>C synonymous_variant S N211N 7.07e-1 B.1.177.73
V1231 4760C>T missense_variant ORF1ab_pp1a S1587L 7.58e-1 B.1.221
V4407 173G>A missense_variant ORF3a S58N 7.56e-1 B.1.221
V3298 19796G>T missense_variant ORF1ab_pp1ab S6599I 6.67e-1 B.1.234
V1009 3451G>A missense_variant ORF1ab_pp1a A1151T 8.16e-1 B.1.258
V1259 4913C>A missense_variant ORF1ab_pp1a T1638N 7.07e-1 B.1.36.17
V1607 6848C>T missense_variant ORF1ab_pp1a T2283I 7.07e-1 B.1.36.17
V1888 8888A>G missense_variant ORF1ab_pp1a Q2963R 1.00e+0 B.1.36.17
V1944 9350C>T missense_variant ORF1ab_pp1a T3117I 1.00e+0 B.1.36.17
V216 304G>A missense_variant ORF1ab_pp1a E102K 1.00e+0 B.1.36.17
V3258 19595C>T missense_variant ORF1ab_pp1ab A6532V 1.00e+0 B.1.36.17
V3525 26C>T missense_variant S P9L 1.00e+0 B.1.36.17
V3578 204_209delACATGT disruptive_inframe_deletion S H69_V70del 1.00e+0 B.1.36.17
V3909 1450G>A missense_variant S E484K 1.00e+0 B.1.36.17
V3945 1668C>A missense_variant S N556K 1.00e+0 B.1.36.17
V3997 1963C>T missense_variant S H655Y 1.00e+0 B.1.36.17
V4143 2848G>A missense_variant S D950N 7.07e-1 B.1.36.17
V5239 -3A>C upstream_gene_variant N None 7.07e-1 B.1.36.17
V5354 250A>G missense_variant N I84V 1.00e+0 B.1.36.17
V6632 5568C>T synonymous_variant ORF1ab_pp1a S1856S 7.07e-1 B.1.36.17
V5219 355G>T missense_variant ORF8 D119Y 7.96e-1 B.1.367
V6108 1758C>T synonymous_variant ORF1ab_pp1a F586F 1.00e+0 B.1.367
V6346 3354C>T synonymous_variant ORF1ab_pp1a V1118V 9.53e-1 B.1.367
V1169 4418C>T missense_variant ORF1ab_pp1a A1473V 7.82e-1 B.1.369
V2349 12347T>C missense_variant ORF1ab_pp1a M4116T 1.00e+0 B.1.369
V2658 14890C>T missense_variant ORF1ab_pp1ab H4964Y 1.00e+0 B.1.369
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 9.43e-1 B.1.369
V4775 373C>T missense_variant M H125Y 8.94e-1 B.1.369
V5068 13G>A missense_variant ORF8 V5I 1.00e+0 B.1.369
V5700 47T>C missense_variant ORF10 L16P 9.35e-1 B.1.369
V7066 8994A>G synonymous_variant ORF1ab_pp1a V2998V 8.75e-1 B.1.369
V9438 120C>T synonymous_variant ORF7a Y40Y 8.53e-1 B.1.369
V9582 105G>T synonymous_variant N A35A 6.61e-1 B.1.369
V1659 7463C>T missense_variant ORF1ab_pp1a S2488F 6.10e-1 B.1.396
V1400 5990C>T missense_variant ORF1ab_pp1a A1997V 6.66e-1 B.1.466.2
V4264 3687G>T missense_variant S M1229I 6.66e-1 B.1.466.2
V94 -26T>C upstream_gene_variant ORF1ab_pp1a None 6.66e-1 B.1.466.2
V1687 7604C>T missense_variant ORF1ab_pp1a S2535L 7.07e-1 B.1.470
V3370 20213G>T missense_variant ORF1ab_pp1ab G6738V 7.07e-1 B.1.470
V4129 2806G>A missense_variant S D936N 1.00e+0 B.1.470
V584 1703C>T missense_variant ORF1ab_pp1a T568I 7.07e-1 B.1.470
V7546 12831T>C synonymous_variant ORF1ab_pp1a A4277A 1.00e+0 B.1.470
V7195 9942C>T synonymous_variant ORF1ab_pp1a N3314N 6.66e-1 B.1.560
V3585 212C>T missense_variant S S71F 1.00e+0 B.1.561
V7102 9294C>T synonymous_variant ORF1ab_pp1a Y3098Y 7.07e-1 B.1.561
V1926 9209C>T missense_variant ORF1ab_pp1a A3070V 1.00e+0 B.1.564
V360 877C>T missense_variant ORF1ab_pp1a L293F 1.00e+0 B.1.564
V3994 1958C>T missense_variant S A653V 1.00e+0 B.1.564
V4675 89C>T missense_variant E T30I 1.00e+0 B.1.564
V4775 373C>T missense_variant M H125Y 8.16e-1 B.1.564
V4888 110C>T missense_variant ORF7a S37F 1.00e+0 B.1.564
V5131 155G>T missense_variant ORF8 R52I 7.07e-1 B.1.564
V5162 202A>T stop_gained ORF8 K68* 7.07e-1 B.1.564
V5171 218A>G missense_variant ORF8 Y73C 7.07e-1 B.1.564
V5390 430G>C missense_variant N D144H 1.00e+0 B.1.564
V564 1652C>T missense_variant ORF1ab_pp1a T551I 1.00e+0 B.1.564
V7260 10500C>T synonymous_variant ORF1ab_pp1a Y3500Y 1.00e+0 B.1.564
V760 2441C>T missense_variant ORF1ab_pp1a T814I 7.07e-1 B.1.564
V9123 3753A>G synonymous_variant S G1251G 1.00e+0 B.1.564
V9584 108A>G synonymous_variant N R36R 1.00e+0 B.1.564
V2405 12746C>T missense_variant ORF1ab_pp1a T4249I 1.00e+0 B.1.565
V4331 67G>T missense_variant ORF3a A23S 7.07e-1 B.1.621
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 6.74e-1 B.1.637
V2162 11024_11028delCTGGT frameshift_variant ORF1ab_pp1a S3675fs 7.50e-1 BA.1.1.10
V2524 13681C>T missense_variant ORF1ab_pp1ab P4561S 7.56e-1 BA.1.1.10
V5308 90_97delAGAACGCA frameshift_variant N E31fs 6.70e-1 BA.1.1.10
V540 1586T>C missense_variant ORF1ab_pp1a I529T 8.16e-1 BA.1.1.15
V5682 8A>G missense_variant ORF10 Y3C 8.16e-1 BA.1.1.15
V2004 9967C>T missense_variant ORF1ab_pp1a R3323C 1.00e+0 BA.1.1.16
V5600 1093C>T missense_variant N P365S 1.00e+0 BA.1.12
V1239 4786C>T missense_variant ORF1ab_pp1a P1596S 1.00e+0 BA.1.14.1
V9694 667C>T synonymous_variant N L223L 1.00e+0 BA.1.14.1
V8547 20667G>T synonymous_variant ORF1ab_pp1ab T6889T 6.17e-1 BA.1.20
V7069 9021C>T synonymous_variant ORF1ab_pp1a N3007N 8.04e-1 BA.2.10.1
V7959 15996C>T synonymous_variant ORF1ab_pp1ab C5332C 8.89e-1 BA.2.10.1
V2371 12491C>T missense_variant ORF1ab_pp1a T4164I 7.45e-1 BA.2.12
V7066 8994A>G synonymous_variant ORF1ab_pp1a V2998V 6.11e-1 BA.2.36
V2230 11335A>G missense_variant ORF1ab_pp1a I3779V 1.00e+0 BA.2.37
V3755 727_732delGCTTTA conservative_inframe_deletion S A243_L244del 1.00e+0 BA.2.37
V5807 *4385C>T downstream_gene_variant S None 1.00e+0 BA.2.37
V3824 1037G>C missense_variant S R346T 7.06e-1 BA.2.38.2
V8007 16365G>A synonymous_variant ORF1ab_pp1ab K5455K 1.00e+0 BA.2.40.1
V9421 21G>A synonymous_variant ORF7a L7L 1.00e+0 BA.2.40.1
V2642 14696A>T missense_variant ORF1ab_pp1ab N4899I 1.00e+0 BA.2.44
V7472 12174C>T synonymous_variant ORF1ab_pp1a P4058P 1.00e+0 BA.2.44
V9370 490C>T synonymous_variant M L164L 1.00e+0 BA.2.44
V8701 534C>T synonymous_variant S D178D 7.07e-1 BA.2.49
V2337 12248C>T missense_variant ORF1ab_pp1a T4083M 1.00e+0 BA.2.50
V3566 156G>T missense_variant S Q52H 1.00e+0 BA.2.56
V5293 71C>T missense_variant N T24I 1.00e+0 BA.2.5
V3977 1865T>C missense_variant S V622A 1.00e+0 BA.2.75
V5202 326dupT frameshift_variant ORF8 L109fs 1.00e+0 BA.2.75
V8377 19110C>T synonymous_variant ORF1ab_pp1ab F6370F 1.00e+0 BA.2.81
V869 2945A>G missense_variant ORF1ab_pp1a D982G 1.00e+0 BA.2.81
V3951 1709C>T missense_variant S A570V 1.00e+0 BA.2.9.3
V6049 1302C>T synonymous_variant ORF1ab_pp1a N434N 1.00e+0 BA.2.9.3
V7185 9891C>T synonymous_variant ORF1ab_pp1a D3297D 8.16e-1 BA.2.9.5
V8150 17442G>A synonymous_variant ORF1ab_pp1ab R5814R 8.16e-1 BA.2.9.5
V9151 102G>T synonymous_variant ORF3a T34T 7.07e-1 BA.4.1.4
V1482 6250T>A missense_variant ORF1ab_pp1a L2084I 1.00e+0 BA.4.6.4
V2314 12029C>T missense_variant ORF1ab_pp1a T4010I 7.07e-1 BA.5.1.10
V9354 414C>T synonymous_variant M L138L 1.00e+0 BA.5.1.12
V4707 -22G>T upstream_gene_variant M None 1.00e+0 BA.5.1.1
V9022 3069T>C synonymous_variant S N1023N 1.00e+0 BA.5.1.21
V3372 20219C>T missense_variant ORF1ab_pp1ab S6740F 8.16e-1 BA.5.1.24
V6996 8517C>T synonymous_variant ORF1ab_pp1a S2839S 1.00e+0 BA.5.1.24
V7328 11151C>T synonymous_variant ORF1ab_pp1a L3717L 7.07e-1 BA.5.1.24
V2633 14557C>T missense_variant ORF1ab_pp1ab P4853S 1.00e+0 BA.5.1.26
V3804 851C>T missense_variant S T284I 1.00e+0 BA.5.1.26
V944 3208G>A missense_variant ORF1ab_pp1a G1070S 1.00e+0 BA.5.1.4
V7622 13356C>T synonymous_variant ORF1ab_pp1ab D4452D 1.00e+0 BA.5.1.6
V6651 5721C>T synonymous_variant ORF1ab_pp1a F1907F 1.00e+0 BA.5.1.9
V3744 646C>T missense_variant S L216F 1.00e+0 BA.5.2.12
V7744 14335C>T synonymous_variant ORF1ab_pp1ab L4779L 7.07e-1 BA.5.2.12
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 8.65e-1 BA.5.2.24
V5393 433C>T missense_variant N H145Y 8.32e-1 BA.5.2.24
V9697 684C>T synonymous_variant N N228N 1.00e+0 BA.5.2.24
V3902 1433C>T missense_variant S T478I 1.00e+0 BA.5.2.25
V3988 1925T>G missense_variant S V642G 1.00e+0 BA.5.2.25
V8554 20700C>T synonymous_variant ORF1ab_pp1ab D6900D 1.00e+0 BA.5.2.25
V1863 8672C>T missense_variant ORF1ab_pp1a A2891V 1.00e+0 BA.5.2.26
V8547 20667G>T synonymous_variant ORF1ab_pp1ab T6889T 1.00e+0 BA.5.2.26
V9267 69C>T synonymous_variant E F23F 7.07e-1 BA.5.2.27
V2020 10054C>T missense_variant ORF1ab_pp1a L3352F 7.07e-1 BA.5.2.34
V1321 5408C>T missense_variant ORF1ab_pp1a P1803L 1.00e+0 BA.5.2.36
V7038 8820A>G synonymous_variant ORF1ab_pp1a E2940E 1.00e+0 BA.5.2.36
V8390 19212A>G synonymous_variant ORF1ab_pp1ab L6404L 1.00e+0 BA.5.3.3
V9481 318A>T synonymous_variant ORF7a A106A 1.00e+0 BA.5.3.3
V6278 2865C>T synonymous_variant ORF1ab_pp1a Y955Y 1.00e+0 BA.5.3.5
V7158 9714C>T synonymous_variant ORF1ab_pp1a L3238L 1.00e+0 BA.5.3.5
V4438 232C>T missense_variant ORF3a H78Y 7.07e-1 BA.5.3
V8018 16444C>T synonymous_variant ORF1ab_pp1ab L5482L 7.07e-1 BA.5.3
V4549 530G>T missense_variant ORF3a S177I 1.00e+0 BA.5.5.1
V5677 -3C>T upstream_gene_variant ORF10 None 1.00e+0 BA.5.5.2
V1147 4221G>T missense_variant ORF1ab_pp1a K1407N 1.00e+0 BA.5.6.2
V1258 4910C>T missense_variant ORF1ab_pp1a T1637I 1.00e+0 BA.5.6.2
V6007 978T>C synonymous_variant ORF1ab_pp1a C326C 7.07e-1 BA.5.6.2
V9394 645C>T synonymous_variant M D215D 1.00e+0 BA.5.6.2
V159 163G>A missense_variant ORF1ab_pp1a E55K 8.16e-1 BA.5.8
V7621 13353G>A synonymous_variant ORF1ab_pp1ab K4451K 1.00e+0 BA.5.8
V2961 17482C>T missense_variant ORF1ab_pp1ab P5828S 7.07e-1 BE.10
V8252 18198G>T synonymous_variant ORF1ab_pp1ab P6066P 7.07e-1 BE.10
V2583 14030G>A missense_variant ORF1ab_pp1ab R4677H 9.51e-1 BE.1.1.2
V5543 808G>T missense_variant N V270L 9.46e-1 BE.1.1.2
V7530 12699A>G synonymous_variant ORF1ab_pp1a G4233G 7.24e-1 BE.1.1.2
V8330 18717C>T synonymous_variant ORF1ab_pp1ab H6239H 7.69e-1 BE.1.1.2
V5493 640G>T missense_variant N G214C 6.12e-1 BE.1
V5812 *4393G>T downstream_gene_variant S None 7.07e-1 BF.11
V798 2645C>T missense_variant ORF1ab_pp1a T882I 8.90e-1 BF.14
V8782 1185C>T synonymous_variant S V395V 8.16e-1 BF.14
V3243 19423C>T missense_variant ORF1ab_pp1ab P6475S 8.16e-1 BF.21
V2015 10031C>T missense_variant ORF1ab_pp1a S3344F 7.14e-1 BF.26
V1646 7217C>T missense_variant ORF1ab_pp1a S2406L 1.00e+0 BF.31
V2815 16469C>T missense_variant ORF1ab_pp1ab S5490L 1.00e+0 BF.32
V3658 448A>G missense_variant S K150E 1.00e+0 BF.3
V7062 8958C>T synonymous_variant ORF1ab_pp1a H2986H 6.32e-1 BF.3
V7369 11487C>T synonymous_variant ORF1ab_pp1a L3829L 7.07e-1 BF.7.14
V8120 17199C>T synonymous_variant ORF1ab_pp1ab R5733R 1.00e+0 BF.7.14
V1462 6206C>T missense_variant ORF1ab_pp1a T2069I 6.38e-1 BF.7.5
V8681 363T>C synonymous_variant S N121N 6.46e-1 BF.7.5
V3644 436_438delCAC conservative_inframe_deletion S H146del 1.00e+0 BF.7.8
V6101 1695C>T synonymous_variant ORF1ab_pp1a A565A 1.00e+0 BF.7.8
V6180 2205C>T synonymous_variant ORF1ab_pp1a A735A 7.07e-1 BF.7.8
V3964 1811C>T missense_variant S T604I 1.00e+0 B
V4342 85G>T missense_variant ORF3a V29F 7.07e-1 BN.1.2
V4747 205G>T missense_variant M A69S 1.00e+0 BN.1.2
V5695 29C>T missense_variant ORF10 P10L 7.07e-1 BN.1.3.1
V8476 20019C>T synonymous_variant ORF1ab_pp1ab F6673F 1.00e+0 BN.1.4
V7142 9621C>T synonymous_variant ORF1ab_pp1a Y3207Y 1.00e+0 BQ.1.1.10
V7484 12327T>C synonymous_variant ORF1ab_pp1a V4109V 6.12e-1 BQ.1.1.10
V5627 1147C>T missense_variant N P383S 7.07e-1 BQ.1.1.11
V1028 3514A>G missense_variant ORF1ab_pp1a N1172D 7.07e-1 BQ.1.1.15
V3139 18673G>T missense_variant ORF1ab_pp1ab G6225C 1.00e+0 BQ.1.1.15
V330 694C>T missense_variant ORF1ab_pp1a R232C 1.00e+0 BQ.1.1.15
V178 245_250delGTCATG disruptive_inframe_deletion ORF1ab_pp1a G82_H83del 7.07e-1 BQ.1.1.23
V7957 15981G>A synonymous_variant ORF1ab_pp1ab G5327G 7.07e-1 BQ.1.1.31
V4443 255G>T missense_variant ORF3a L85F 7.56e-1 BQ.1.1.3
V7921 15688C>T synonymous_variant ORF1ab_pp1ab L5230L 6.66e-1 BQ.1.1.3
V7480 12249G>T synonymous_variant ORF1ab_pp1a T4083T 7.07e-1 BQ.1.13
V1623 7030G>A missense_variant ORF1ab_pp1a A2344T 1.00e+0 BQ.1.1.4
V2686 15122C>T missense_variant ORF1ab_pp1ab S5041L 7.07e-1 BQ.1.1.6
V1245 4825C>T missense_variant ORF1ab_pp1a P1609S 7.50e-1 BQ.1.23
V4110 2572C>A missense_variant S L858I 8.66e-1 BQ.1.23
V5136 164C>T missense_variant ORF8 A55V 6.12e-1 BQ.1.23
V4175 3232G>A missense_variant S A1078T 1.00e+0 BQ.1.3
V7477 12219C>T synonymous_variant ORF1ab_pp1a V4073V 7.07e-1 BQ.1.3
V3811 922G>T missense_variant S V308L 1.00e+0 CH.1.1.2
V379 926C>T missense_variant ORF1ab_pp1a P309L 7.14e-1 CH.1.1.3
V552 1624C>T missense_variant ORF1ab_pp1a R542C 7.74e-1 CH.1.1
V6446 4191C>T synonymous_variant ORF1ab_pp1a A1397A 7.07e-1 CL.1
V9159 129C>T synonymous_variant ORF3a F43F 6.32e-1 CL.1
V5137 167C>A missense_variant ORF8 P56H 1.00e+0 CM.2
V5627 1147C>T missense_variant N P383S 1.00e+0 CM.8.1
V2559 13919C>T missense_variant ORF1ab_pp1ab T4640I 7.07e-1 D.2
V2136 10934C>T missense_variant ORF1ab_pp1a A3645V 7.07e-1 P.2
V3438 20744C>T missense_variant ORF1ab_pp1ab T6915I 7.07e-1 XBB.1.2
V3115 18481G>T missense_variant ORF1ab_pp1ab V6161F 1.00e+0 XBF
V3623 394G>C missense_variant S E132Q 1.00e+0 XBF
V1277 5036C>T missense_variant ORF1ab_pp1a A1679V 1.00e+0 A.19
V189 248A>G missense_variant ORF1ab_pp1a H83R 7.04e-1 A.19
V4130 2806G>C missense_variant S D936H 1.00e+0 A.19
V4264 3687G>T missense_variant S M1229I 1.00e+0 A.19
V4386 142G>T missense_variant ORF3a V48F 7.04e-1 A.19
V573 1679G>A missense_variant ORF1ab_pp1a R560H 7.04e-1 A.19
V7099 9267C>T synonymous_variant ORF1ab_pp1a F3089F 7.04e-1 A.19
V8280 18399T>C synonymous_variant ORF1ab_pp1ab C6133C 7.04e-1 A.19
V8535 20559C>T synonymous_variant ORF1ab_pp1ab N6853N 1.00e+0 A.19
V8642 165C>T synonymous_variant S F55F 7.04e-1 A.19
V889 2996C>T missense_variant ORF1ab_pp1a T999I 7.04e-1 A.19
V8963 2565T>C synonymous_variant S F855F 7.04e-1 A.19
V9375 525G>A synonymous_variant M T175T 1.00e+0 A.19
V9495 51G>T synonymous_variant ORF7b L17L 1.00e+0 A.19
V9640 420T>C synonymous_variant N N140N 7.04e-1 A.19
V260 421_429delAAGTCATTT conservative_inframe_deletion ORF1ab_pp1a K141_F143del 7.06e-1 AY.112.3
V4428 207G>T missense_variant ORF3a W69C 1.00e+0 AY.112.3
V8132 17286C>T synonymous_variant ORF1ab_pp1ab L5762L 7.06e-1 AY.112.3
V1134 4134G>T missense_variant ORF1ab_pp1a M1378I 1.00e+0 AY.23.2
V3439 20746G>A missense_variant ORF1ab_pp1ab V6916I 8.15e-1 AY.23.2
V5405 481C>T missense_variant N L161F 1.00e+0 AY.4.1
V1316 5363C>T missense_variant ORF1ab_pp1a T1788M 1.00e+0 AY.75.2
V2021 10058A>G missense_variant ORF1ab_pp1a K3353R 7.06e-1 AY.75.2
V2163 11023_11031delTCTGGTTTT conservative_inframe_deletion ORF1ab_pp1a S3675_F3677del 1.00e+0 AY.75.2
V2897 16995G>T missense_variant ORF1ab_pp1ab E5665D 1.00e+0 AY.75.2
V342 794C>T missense_variant ORF1ab_pp1a T265I 1.00e+0 AY.75.2
V3742 644A>G missense_variant S D215G 7.06e-1 AY.75.2
V3751 725_733delTTGCTTTAC disruptive_inframe_deletion S L242_L244del 7.06e-1 AY.75.2
V7337 11241A>G synonymous_variant ORF1ab_pp1a V3747V 1.00e+0 AY.75.2
V7380 11547C>A synonymous_variant ORF1ab_pp1a G3849G 1.00e+0 AY.75.2
V8449 19719C>T synonymous_variant ORF1ab_pp1ab V6573V 7.06e-1 AY.75.2
V8518 20406G>A synonymous_variant ORF1ab_pp1ab A6802A 1.00e+0 AY.75.2
V1406 6020C>T missense_variant ORF1ab_pp1a T2007I 1.00e+0 B.1.1.347
V1509 6362C>T missense_variant ORF1ab_pp1a T2121I 1.00e+0 B.1.1.347
V1570 6671C>T missense_variant ORF1ab_pp1a S2224F 1.00e+0 B.1.1.347
V2065 10490C>T missense_variant ORF1ab_pp1a A3497V -1.00e+0 B.1.1.347
V2283 11810A>G missense_variant ORF1ab_pp1a N3937S 1.00e+0 B.1.1.347
V6783 6735C>T synonymous_variant ORF1ab_pp1a Y2245Y -7.01e-1 B.1.1.347
V8036 16623C>T synonymous_variant ORF1ab_pp1ab Y5541Y 1.00e+0 B.1.1.347
V9160 132A>G synonymous_variant ORF3a G44G 1.00e+0 B.1.1.347
V1334 5465C>T missense_variant ORF1ab_pp1a T1822I 1.00e+0 B.1.1.368
V4918 184C>T stop_gained ORF7a Q62* 1.00e+0 B.1.1.368
V5206 337G>T missense_variant ORF8 D113Y 1.00e+0 B.1.1.368
V6178 2190C>T synonymous_variant ORF1ab_pp1a L730L 1.00e+0 B.1.1.368
V6877 7569C>T synonymous_variant ORF1ab_pp1a N2523N 1.00e+0 B.1.1.368
V8161 17502C>T synonymous_variant ORF1ab_pp1ab V5834V 1.00e+0 B.1.1.368
V8647 195C>T synonymous_variant S F65F 1.00e+0 B.1.1.368
V8929 2367C>T synonymous_variant S Y789Y 1.00e+0 B.1.1.368
V1142 4190C>T missense_variant ORF1ab_pp1a A1397V 1.00e+0 B.1.1.398
V262 424T>C missense_variant ORF1ab_pp1a S142P 1.00e+0 B.1.1.398
V3351 20141C>T missense_variant ORF1ab_pp1ab P6714L 1.00e+0 B.1.1.398
V5841 48C>T synonymous_variant ORF1ab_pp1a L16L 1.00e+0 B.1.1.398
V632 1882C>T missense_variant ORF1ab_pp1a L628F 1.00e+0 B.1.1.398
V99 -24G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.1.398
V3412 20497A>G missense_variant ORF1ab_pp1ab T6833A 9.10e-1 B.1.1.47
V4509 393G>T missense_variant ORF3a W131C 1.00e+0 B.1.1.47
V7925 15696C>T synonymous_variant ORF1ab_pp1ab A5232A 6.05e-1 B.1.1.47
V8721 663G>T synonymous_variant S S221S 1.00e+0 B.1.1.47
V2143 10957G>T missense_variant ORF1ab_pp1a V3653F 9.49e-1 B.1.1.500
V2815 16469C>T missense_variant ORF1ab_pp1ab S5490L -6.88e-1 B.1.1.500
V3264 19627G>T missense_variant ORF1ab_pp1ab D6543Y 8.94e-1 B.1.1.500
V388 965A>G missense_variant ORF1ab_pp1a K322R 1.00e+0 B.1.1.500
V5163 205T>C missense_variant ORF8 S69P 8.94e-1 B.1.1.500
V578 1692G>T missense_variant ORF1ab_pp1a K564N 9.49e-1 B.1.1.500
V757 2410C>T missense_variant ORF1ab_pp1a P804S -7.18e-1 B.1.1.500
V8144 17412C>T synonymous_variant ORF1ab_pp1ab I5804I 1.00e+0 B.1.1.500
V8359 18922C>T synonymous_variant ORF1ab_pp1ab L6308L 8.94e-1 B.1.1.500
V2467 13307G>T missense_variant ORF1ab_pp1ab G4436V 7.06e-1 B.1.413
V8799 1296C>T synonymous_variant S C432C 7.06e-1 B.1.413
V6481 4455G>T synonymous_variant ORF1ab_pp1a A1485A 1.00e+0 B.1.468
V7101 9276C>T synonymous_variant ORF1ab_pp1a L3092L 1.00e+0 B.1.468
V7575 13005T>C synonymous_variant ORF1ab_pp1a D4335D 1.00e+0 B.1.468
V8449 19719C>T synonymous_variant ORF1ab_pp1ab V6573V 1.00e+0 B.1.468
V3369 20210C>T missense_variant ORF1ab_pp1ab T6737I 1.00e+0 B.1.480
V4836 165G>T missense_variant ORF6 E55D 1.00e+0 B.1.480
V5604 1100A>G missense_variant N E367G 1.00e+0 B.1.480
V5725 *4302C>T downstream_gene_variant S None 7.06e-1 B.1.480
V6354 3430C>T synonymous_variant ORF1ab_pp1a L1144L 1.00e+0 B.1.480
V7185 9891C>T synonymous_variant ORF1ab_pp1a D3297D 1.00e+0 B.1.480
V7476 12208C>T synonymous_variant ORF1ab_pp1a L4070L 1.00e+0 B.1.480
V1625 7031C>T missense_variant ORF1ab_pp1a A2344V -9.20e-1 B.1.639
V1785 8276C>T missense_variant ORF1ab_pp1a A2759V -9.60e-1 B.1.639
V1898 8939A>G missense_variant ORF1ab_pp1a D2980G -9.60e-1 B.1.639
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F -9.20e-1 B.1.639
V1989 9851C>T missense_variant ORF1ab_pp1a T3284I -9.60e-1 B.1.639
V2777 16111C>A missense_variant ORF1ab_pp1ab P5371T 1.00e+0 B.1.639
V3933 1558G>T missense_variant S A520S -9.20e-1 B.1.639
V4013 2030A>G missense_variant S Q677R -9.60e-1 B.1.639
V4350 95C>T missense_variant ORF3a T32I -9.20e-1 B.1.639
V445 1192C>T missense_variant ORF1ab_pp1a R398C -9.60e-1 B.1.639
V4535 512C>T missense_variant ORF3a S171L -9.20e-1 B.1.639
V4581 637C>A missense_variant ORF3a Q213K 1.00e+0 B.1.639
V4609 718C>T missense_variant ORF3a P240S 1.00e+0 B.1.639
V4624 766_769delGTTA frameshift_variant ORF3a V256fs -9.60e-1 B.1.639
V4629 770delA frameshift_variant ORF3a N257fs 9.24e-1 B.1.639
V4978 295C>T missense_variant ORF7a P99S -8.81e-1 B.1.639
V5487 632C>T missense_variant N A211V -9.60e-1 B.1.639
V622 1856C>T missense_variant ORF1ab_pp1a T619I 1.00e+0 B.1.639
V6789 6786C>T synonymous_variant ORF1ab_pp1a Y2262Y -8.81e-1 B.1.639
V7701 14031T>C synonymous_variant ORF1ab_pp1ab R4677R 1.00e+0 B.1.639
V8636 129C>T synonymous_variant S F43F -9.20e-1 B.1.639
V6992 8493T>C synonymous_variant ORF1ab_pp1a H2831H 1.00e+0 BA.1.17.1
V1277 5036C>T missense_variant ORF1ab_pp1a A1679V 1.00e+0 BA.2.17
V6164 2133G>A synonymous_variant ORF1ab_pp1a T711T 7.06e-1 BA.2.17
V7234 10296T>C synonymous_variant ORF1ab_pp1a T3432T 7.06e-1 BA.2.17
V8944 2461C>T synonymous_variant S L821L 1.00e+0 BA.3.1
V9777 1038C>T synonymous_variant N F346F 1.00e+0 BA.4.1.2
V1989 9851C>T missense_variant ORF1ab_pp1a T3284I 1.00e+0 BF.7.10
V4121 2675C>T missense_variant S A892V 1.00e+0 BF.7.10
V2352 12386C>T missense_variant ORF1ab_pp1a T4129I 8.65e-1 BN.1.1.1
V2819 16486C>T missense_variant ORF1ab_pp1ab P5496S 1.00e+0 BN.1.1.1
V7483 12294C>T synonymous_variant ORF1ab_pp1a I4098I 1.00e+0 BN.1.1.1
V8520 20415G>A synonymous_variant ORF1ab_pp1ab P6805P 1.00e+0 BN.1.1.1
V1260 4913C>T missense_variant ORF1ab_pp1a T1638I 1.00e+0 BN.1.6
V5303 88_96delGGAGAACGC conservative_inframe_deletion N G30_R32del 1.00e+0 BN.1.6
V8105 17109C>T synonymous_variant ORF1ab_pp1ab A5703A 1.00e+0 BN.1.6
V2996 17765C>T missense_variant ORF1ab_pp1ab A5922V 7.06e-1 BQ.1.27
V1278 5045C>T missense_variant ORF1ab_pp1a T1682I 1.00e+0 BQ.1.4
V3663 455G>T missense_variant S W152L 1.00e+0 BQ.1.4
V3693 541G>A missense_variant S G181R 1.00e+0 BQ.1.4
V474 1307C>T missense_variant ORF1ab_pp1a T436I 7.06e-1 BQ.1.4
V4842 -5C>T upstream_gene_variant ORF7a None 7.06e-1 BQ.1.4
V6939 8025C>T synonymous_variant ORF1ab_pp1a L2675L 1.00e+0 BQ.1.4
V7561 12945T>C synonymous_variant ORF1ab_pp1a N4315N 1.00e+0 CH.1
V110 -10G>A upstream_gene_variant ORF1ab_pp1a None 1.00e+0 CM.12
V6667 5883T>A synonymous_variant ORF1ab_pp1a P1961P 1.00e+0 CM.12
V3319 19970C>T missense_variant ORF1ab_pp1ab P6657L 1.00e+0 CM.4
V395 1003G>A missense_variant ORF1ab_pp1a D335N 1.00e+0 CM.4
V2795 16264G>T missense_variant ORF1ab_pp1ab V5422F -1.00e+0 P.4
V4390 148G>A missense_variant ORF3a V50I 1.00e+0 P.4
V4967 280C>T stop_gained ORF7a Q94* -1.00e+0 P.4
V7358 11409C>T synonymous_variant ORF1ab_pp1a Y3803Y -1.00e+0 P.4





Manual curation of mutation (11743C>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