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The current mutation

ID: V850
DNA: 2857G>T
Protein: D953Y
Position: 3122








COV2Var annotation categories







Summary information of mutation (2857G>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   3122
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 2857G>T
  Ref Seq: G
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: D953Y
  Protein 3-letter Mutation: Asp953Tyr

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 (2857G>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.1.177.4 75 41 5.47e-1
2020-10 B.1.2 75 7 9.33e-2
2020-10 B.1.1.170 75 5 6.67e-2
2020-11 B.1.177.4 180 77 4.28e-1
2020-11 B.1.2 180 40 2.22e-1
2020-11 B.1.1.432 180 18 1.00e-1
2020-12 B.1 143 37 2.59e-1
2020-12 B.1.1.432 143 30 2.10e-1
2020-12 B.1.177 143 16 1.12e-1
2020-03 A.1 9 8 8.89e-1
2020-03 B.1 9 1 1.11e-1
2020-04 B.1 12 7 5.83e-1
2020-04 A.1 12 1 8.33e-2
2020-04 B.1.157 12 1 8.33e-2
2020-05 B.1.1 11 4 3.64e-1
2020-05 L.2 11 2 1.82e-1
2020-05 B.1 11 1 9.09e-2
2020-06 B.1.39 22 9 4.09e-1
2020-06 B.1.242 22 4 1.82e-1
2020-06 B.1.1 22 2 9.09e-2
2020-07 B.1 7 2 2.86e-1
2020-07 B.1.1.135 7 2 2.86e-1
2020-07 B.1.1.432 7 1 1.43e-1
2020-08 B.1.1.135 9 2 2.22e-1
2020-08 B.1.1.241 9 2 2.22e-1
2020-08 B.1.1 9 1 1.11e-1
2020-09 B.1.1.322 30 6 2.00e-1
2020-09 B.1.1.432 30 5 1.67e-1
2020-09 B.1.1.33 30 4 1.33e-1
2021-01 B.1.177 252 59 2.34e-1
2021-01 B.1.1.170 252 44 1.75e-1
2021-01 B.1.1.432 252 30 1.19e-1
2021-10 AY.4 691 363 5.25e-1
2021-10 AY.42 691 90 1.30e-1
2021-10 AY.122 691 80 1.16e-1
2021-11 AY.4 1063 351 3.30e-1
2021-11 AY.42 1063 262 2.46e-1
2021-11 AY.54 1063 173 1.63e-1
2021-12 AY.4 632 207 3.28e-1
2021-12 AY.43 632 135 2.14e-1
2021-12 AY.42 632 102 1.61e-1
2021-02 B.1.177.83 224 54 2.41e-1
2021-02 B.1.1.7 224 32 1.43e-1
2021-02 B.1.1.432 224 27 1.21e-1
2021-03 B.1.1.519 317 142 4.48e-1
2021-03 B.1.1.7 317 69 2.18e-1
2021-03 B.1.177.83 317 38 1.20e-1
2021-04 B.1.1.519 300 150 5.00e-1
2021-04 B.1.1.7 300 115 3.83e-1
2021-04 B.1.526 300 7 2.33e-2
2021-05 B.1.1.7 94 44 4.68e-1
2021-05 B.1.617.2 94 27 2.87e-1
2021-05 B.1.1.519 94 8 8.51e-2
2021-06 B.1.617.2 61 12 1.97e-1
2021-06 P.1 61 8 1.31e-1
2021-06 B.1.1.7 61 7 1.15e-1
2021-07 AY.42 102 28 2.75e-1
2021-07 AY.20 102 18 1.76e-1
2021-07 AY.21 102 8 7.84e-2
2021-08 AY.4 433 198 4.57e-1
2021-08 AY.42 433 68 1.57e-1
2021-08 AY.20 433 44 1.02e-1
2021-09 AY.4 540 276 5.11e-1
2021-09 AY.42 540 69 1.28e-1
2021-09 AY.122 540 53 9.81e-2
2022-01 BA.1.1 115 17 1.48e-1
2022-01 AY.42 115 14 1.22e-1
2022-01 AY.43 115 13 1.13e-1
2022-10 BA.2.75.2 49 22 4.49e-1
2022-10 BA.5.1.12 49 13 2.65e-1
2022-10 BF.7 49 2 4.08e-2
2022-11 CK.1 28 6 2.14e-1
2022-11 BA.2.75.2 28 5 1.79e-1
2022-11 BA.5.1.12 28 4 1.43e-1
2022-12 BF.5 43 5 1.16e-1
2022-12 BA.5.2.6 43 4 9.30e-2
2022-12 BQ.1.23 43 4 9.30e-2
2022-02 BA.1.1 35 11 3.14e-1
2022-02 BA.2 35 7 2.00e-1
2022-02 BA.1 35 4 1.14e-1
2022-03 BA.2 82 62 7.56e-1
2022-03 BA.2.9 82 7 8.54e-2
2022-03 BA.1.14.1 82 3 3.66e-2
2022-04 BA.2 111 82 7.39e-1
2022-04 BA.2.9 111 22 1.98e-1
2022-04 BA.2.3.11 111 3 2.70e-2
2022-05 BA.2 117 103 8.80e-1
2022-05 BA.2.3 117 3 2.56e-2
2022-05 BA.2.9 117 2 1.71e-2
2022-06 BA.2 89 75 8.43e-1
2022-06 BA.5 89 3 3.37e-2
2022-06 BA.2.75 89 2 2.25e-2
2022-07 BA.2 41 19 4.63e-1
2022-07 BA.5.2.2 41 6 1.46e-1
2022-07 BA.5.2.21 41 4 9.76e-2
2022-08 BA.2 22 4 1.82e-1
2022-08 BA.5 22 4 1.82e-1
2022-08 BA.5.1.12 22 3 1.36e-1
2022-09 BA.5.1.12 28 7 2.50e-1
2022-09 BA.5 28 4 1.43e-1
2022-09 BA.2.75.2 28 3 1.07e-1
2023-01 BQ.1.1 32 7 2.19e-1
2023-01 BQ.1.5 32 4 1.25e-1
2023-01 BF.5 32 3 9.38e-2
2023-02 BQ.1.1 23 15 6.52e-1
2023-02 XBB.1.5 23 3 1.30e-1
2023-02 XBB.1.9.1 23 2 8.70e-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
V850 AY.21 1.12e-2 4 2021-4-20 2021-12-24
V850 AY.42 2.19e-2 638 2020-10-15 2022-7-19
V850 AY.54 1.61e-2 228 2021-2-9 2022-2-10
V850 B.1.1.170 9.87e-2 77 2020-7-19 2021-6-28
V850 B.1.1.27 1.17e-2 2 2020-3-21 2021-3-22
V850 B.1.1.322 2.65e-2 3 2020-4-13 2021-5-12
V850 B.1.1.432 1.56e-1 124 2020-4-24 2021-5-8
V850 B.1.1.519 1.32e-2 331 2020-8-28 2022-9-27
V850 B.1.160.28 4.21e-2 13 2020-9-5 2021-6-8
V850 B.1.177.4 2.92e-2 129 2020-6-3 2021-3-16
V850 B.1.177.83 1.80e-1 110 2020-8-25 2021-6-8
V850 B.1.179 1.60e-2 4 2020-3-9 2021-4-29
V850 B.1.242 7.84e-2 4 2020-4-21 2021-8-20
V850 B.1.39 4.47e-2 11 2020-3-9 2020-6-29
V850 B.1.450 4.40e-2 4 2020-3-14 2020-9-29
V850 B.1.538 3.49e-2 3 2020-5-16 2021-6-17
V850 BA.5.1.12 1.17e-2 27 2022-2-8 2023-2-18
V850 C.16 7.05e-2 58 2020-6-26 2021-6-2
V850 L.2 2.44e-2 2 2020-3-23 2021-1-21






Examining mutation (2857G>T) found in abundant sequences of non-human animal hosts

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

Animal host Lineage Source region Collection date Accession ID




Association between mutation (2857G>T) and patients of different ages, genders, and statuses

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

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

Attribute Effect Estimate SE Z-value P-value Direction
Patient status Ambulatory -2.21e+0 1.04e+0 -2.13e+0 3.33e-2 Decrease
Deceased -1.18e+0 1.04e+0 -1.14e+0 2.54e-1 Decrease
Homebound 3.63e+0 6.03e-1 6.03e+0 1.66e-9 Increase
Hospitalized -5.84e-2 3.34e-1 -1.75e-1 8.61e-1 Decrease
Mild 1.87e+0 4.15e-1 4.50e+0 6.73e-6 Increase
Recovered -8.24e-1 3.48e-1 -2.37e+0 1.79e-2 Decrease

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

Attribute Effect Estimate SE Z-value P-value Direction
Patient age, years 0-17 -2.06e-2 1.22e-1 -1.69e-1 8.66e-1 Decrease
18-39 -1.77e-1 7.21e-2 -2.45e+0 1.41e-2 Decrease
40-64 7.18e-2 7.22e-2 9.94e-1 3.20e-1 Increase
65-84 8.85e-2 1.00e-1 8.83e-1 3.77e-1 Increase
>=85 3.83e-1 1.54e-1 2.49e+0 1.28e-2 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 -2.87e-2 6.93e-2 -4.14e-1 6.79e-1 Decrease





Investigating natural selection at mutation (2857G>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
nsp3 2720 8554 1945 135 0.00e+0 AY.29 MEME

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
nsp3 2720 8554 1945 135 2.00e-2 9.60e-1 AZ.2 FUBAR




Alterations in protein physicochemical properties induced by mutation (2857G>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 490037 6.05 545040 88.99 -0.023
Reference ORF1ab_pp1a 489988.91 6.04 543550 88.99 -0.023




Alterations in protein stability induced by mutation (2857G>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
D953Y ORF1ab_pp1a Point 953 1.54 Increase 7 25 Environment
D953Y ORF1ab_pp1a Point 953 1.69 Increase 7.4 37 Internal




Impact on protein function induced by mutation (2857G>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
D953Y ORF1ab_pp1a Point 0.056 Gain of Phosphorylation at D953 (Pr = 0.80 | P = 7.4e-04)
Altered MoRF (Pr = 0.32 | P = 0.02)
Gain of Strand (Pr = 0.26 | P = 0.04)
Loss of Ubiquitylation at K958 (Pr = 0.17 | P = 0.02)
Gain of Acetylation at K958 (Pr = 0.16 | P = 0.08)
Loss of Sulfation at Y955 (Pr = 0.12 | P = 2.0e-03)
Loss of Methylation at K958 (Pr = 0.08 | P = 0.07)




Exploring mutation (2857G>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 (2857G>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
D953Y ORF1ab_pp1a 3122 Chymotrypsin-high specificity GTEYDYQGKP (pos: 953)
 NA
D953Y ORF1ab_pp1a 3122 Proteinase K GTEYDYQGKP (pos: 953)
 NA
D953Y ORF1ab_pp1a 3122 Asp-N endopeptidase NA
 YGTEDDYQGK (pos: 952)
D953Y ORF1ab_pp1a 3122 Chymotrypsin-low specificity GTEYDYQGKP (pos: 953)
 NA
D953Y ORF1ab_pp1a 3122 Formic acid NA
 GTEDDYQGKP (pos: 953)
D953Y ORF1ab_pp1a 3122 Pepsin (pH>2) YGTEYDYQGK (pos: 952)
GTEYDYQGKP (pos: 953)
 NA
D953Y ORF1ab_pp1a 3122 Asp-N endopeptidase + N-terminal Glu NA
 YGTEDDYQGK (pos: 952)




Impact of spike protein mutation (2857G>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 (2857G>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 (2857G>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 (2857G>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
V371 905C>T missense_variant ORF1ab_pp1a S302F 7.36e-1 B.1.177
V5446 584G>T missense_variant N R195I 7.06e-1 B.1.177
V4516 427G>T missense_variant ORF3a A143S 7.94e-1 AY.43
V5297 77G>A missense_variant N S26N 8.71e-1 AY.43
V8431 19590C>T synonymous_variant ORF1ab_pp1ab D6530D 7.24e-1 AY.29
V479 1325G>A missense_variant ORF1ab_pp1a G442D 7.07e-1 BA.1.1.18
V562 1649G>A missense_variant ORF1ab_pp1a R550H 6.71e-1 BA.1.1.2
V1429 6093G>T missense_variant ORF1ab_pp1a E2031D 6.47e-1 AY.122
V9634 387C>T synonymous_variant N G129G 7.76e-1 AY.122
V4967 280C>T stop_gained ORF7a Q94* 6.83e-1 AY.20
V871 2950A>G missense_variant ORF1ab_pp1a S984G 7.46e-1 AY.47
V7779 14529C>T synonymous_variant ORF1ab_pp1ab S4843S 7.07e-1 B.1
V8116 17175C>T synonymous_variant ORF1ab_pp1ab D5725D 6.28e-1 B.1
V9688 642C>T synonymous_variant N G214G 7.40e-1 B.1
V2695 15187G>T missense_variant ORF1ab_pp1ab G5063C 7.45e-1 BF.7
V9767 991T>C synonymous_variant N L331L 6.12e-1 XBB.1.5
V1987 9838A>G missense_variant ORF1ab_pp1a M3280V 1.00e+0 AY.106
V2314 12029C>T missense_variant ORF1ab_pp1a T4010I 1.00e+0 AY.106
V4281 3754T>C missense_variant S S1252P 1.00e+0 AY.106
V2092 10678G>A missense_variant ORF1ab_pp1a V3560I 7.07e-1 AY.107
V2819 16486C>T missense_variant ORF1ab_pp1ab P5496S 7.07e-1 AY.107
V1175 4498C>T missense_variant ORF1ab_pp1a H1500Y 7.07e-1 AY.116.1
V4765 253G>T missense_variant M A85S 7.07e-1 AY.116
V6723 6198G>T synonymous_variant ORF1ab_pp1a V2066V 1.00e+0 AY.116
V8430 19587G>A synonymous_variant ORF1ab_pp1ab V6529V 1.00e+0 AY.116
V3523 24G>T missense_variant S L8F 7.27e-1 AY.118
V4573 604G>T missense_variant ORF3a V202L 6.23e-1 AY.118
V83 -45T>C upstream_gene_variant ORF1ab_pp1a None 6.96e-1 AY.118
V3305 19840C>T missense_variant ORF1ab_pp1ab L6614F 1.00e+0 AY.121.1
V5578 1001C>T missense_variant N T334I 1.00e+0 AY.121.1
V6014 1023C>T synonymous_variant ORF1ab_pp1a C341C 1.00e+0 AY.121.1
V6863 7446T>C synonymous_variant ORF1ab_pp1a N2482N 1.00e+0 AY.121.1
V8889 2004A>T synonymous_variant S A668A 7.07e-1 AY.121
V2594 14143C>T missense_variant ORF1ab_pp1ab P4715S 8.75e-1 AY.13
V5713 88G>T missense_variant ORF10 V30L 8.75e-1 AY.13
V7795 14661C>T synonymous_variant ORF1ab_pp1ab V4887V 8.16e-1 AY.13
V3763 733C>T missense_variant S H245Y 7.07e-1 AY.15
V4139 2827A>C missense_variant S S943R 7.07e-1 AY.15
V8172 17586C>T synonymous_variant ORF1ab_pp1ab G5862G 8.16e-1 AY.15
V7215 10143C>T synonymous_variant ORF1ab_pp1a Y3381Y 1.00e+0 AY.16
V2513 13598C>T missense_variant ORF1ab_pp1ab T4533I 1.00e+0 AY.22
V4888 110C>T missense_variant ORF7a S37F 1.00e+0 AY.22
V7043 8865G>T synonymous_variant ORF1ab_pp1a V2955V 1.00e+0 AY.22
V8840 1668C>T synonymous_variant S N556N 1.00e+0 AY.22
V9654 471C>T synonymous_variant N I157I 1.00e+0 AY.22
V9766 987G>T synonymous_variant N T329T 1.00e+0 AY.22
V7190 9921C>T synonymous_variant ORF1ab_pp1a C3307C 1.00e+0 AY.24
V3022 17911C>T missense_variant ORF1ab_pp1ab P5971S 8.25e-1 AY.33
V1750 7982C>T missense_variant ORF1ab_pp1a S2661F 1.00e+0 AY.34.1.1
V5737 *4322G>T downstream_gene_variant S None 8.16e-1 AY.34.1.1
V2136 10934C>T missense_variant ORF1ab_pp1a A3645V 7.07e-1 AY.34
V4320 53G>A missense_variant ORF3a G18D 7.07e-1 AY.34
V8240 18124C>T synonymous_variant ORF1ab_pp1ab L6042L 1.00e+0 AY.34
V3536 59C>T missense_variant S T20I 7.07e-1 AY.36.1
V7454 12042A>G synonymous_variant ORF1ab_pp1a K4014K 1.00e+0 AY.36.1
V3747 662C>T missense_variant S S221L 1.00e+0 AY.37
V9411 141T>C synonymous_variant ORF6 N47N 1.00e+0 AY.37
V3570 184G>C missense_variant S V62L 1.00e+0 AY.41
V5734 *4321G>T downstream_gene_variant S None 1.00e+0 AY.41
V2996 17765C>T missense_variant ORF1ab_pp1ab A5922V 9.53e-1 AY.42
V5020 40_41delTT frameshift_variant ORF7b L14fs 6.00e-1 AY.42
V6846 7299C>T synonymous_variant ORF1ab_pp1a S2433S 8.89e-1 AY.42
V8429 19575T>C synonymous_variant ORF1ab_pp1ab N6525N 9.34e-1 AY.42
V9429 91T>C synonymous_variant ORF7a L31L 9.33e-1 AY.42
V1206 4639G>T missense_variant ORF1ab_pp1a D1547Y 7.07e-1 AY.43.8
V4516 427G>T missense_variant ORF3a A143S 7.07e-1 AY.43.8
V4898 125G>A missense_variant ORF7a G42D 7.07e-1 AY.43.8
V5297 77G>A missense_variant N S26N 7.07e-1 AY.43.8
V7626 13401C>T synonymous_variant ORF1ab_pp1ab H4467H 7.07e-1 AY.43.8
V2368 12482C>T missense_variant ORF1ab_pp1a T4161I 9.26e-1 AY.4.5
V326 671C>T missense_variant ORF1ab_pp1a T224I 6.54e-1 AY.4.5
V8160 17499T>C synonymous_variant ORF1ab_pp1ab A5833A 9.26e-1 AY.4.5
V2101 10736C>T missense_variant ORF1ab_pp1a T3579I 7.07e-1 AY.45
V6038 1230G>T synonymous_variant ORF1ab_pp1a V410V 7.07e-1 AY.45
V7326 11130A>G synonymous_variant ORF1ab_pp1a T3710T 7.07e-1 AY.45
V9549 309G>A synonymous_variant ORF8 S103S 1.00e+0 AY.45
V8152 17457G>T synonymous_variant ORF1ab_pp1ab V5819V 7.07e-1 AY.53
V1370 5762C>A missense_variant ORF1ab_pp1a P1921Q 1.00e+0 AY.5.4
V2347 12304G>A missense_variant ORF1ab_pp1a V4102I 1.00e+0 AY.5.4
V4128 2800A>G missense_variant S I934V 7.07e-1 AY.5.4
V5093 74G>T missense_variant ORF8 C25F 7.07e-1 AY.5.4
V7291 10755C>T synonymous_variant ORF1ab_pp1a L3585L 7.07e-1 AY.5.4
V7919 15678A>G synonymous_variant ORF1ab_pp1ab P5226P 1.00e+0 AY.5.4
V9338 351C>T synonymous_variant M N117N 1.00e+0 AY.5.4
V1283 5074C>T missense_variant ORF1ab_pp1a P1692S 9.15e-1 AY.54
V2817 16477G>T missense_variant ORF1ab_pp1ab V5493F 7.83e-1 AY.54
V6100 1677G>T synonymous_variant ORF1ab_pp1a V559V 9.93e-1 AY.54
V7100 9270T>C synonymous_variant ORF1ab_pp1a T3090T 7.13e-1 AY.54
V7122 9513C>T synonymous_variant ORF1ab_pp1a S3171S 6.11e-1 AY.54
V5294 73G>T missense_variant N G25C 7.07e-1 AY.57
V1579 6746C>T missense_variant ORF1ab_pp1a A2249V 7.07e-1 AY.67
V2346 12300G>T missense_variant ORF1ab_pp1a Q4100H 7.07e-1 AY.67
V3470 20940G>T missense_variant ORF1ab_pp1ab K6980N 7.07e-1 AY.67
V3747 662C>T missense_variant S S221L 7.07e-1 AY.67
V5096 79C>T stop_gained ORF8 Q27* 7.07e-1 AY.67
V9694 667C>T synonymous_variant N L223L 7.07e-1 AY.67
V4569 584C>T missense_variant ORF3a S195F 8.94e-1 AY.69
V2346 12300G>T missense_variant ORF1ab_pp1a Q4100H 6.12e-1 AY.75
V3470 20940G>T missense_variant ORF1ab_pp1ab K6980N 6.12e-1 AY.75
V9694 667C>T synonymous_variant N L223L 6.12e-1 AY.75
V9564 39C>T synonymous_variant N P13P 7.07e-1 AY.7
V6900 7752G>T synonymous_variant ORF1ab_pp1a A2584A 1.00e+0 AY.82
V9634 387C>T synonymous_variant N G129G 1.00e+0 AY.82
V240 360G>T missense_variant ORF1ab_pp1a K120N 6.71e-1 AY.85
V5281 53G>T missense_variant N G18V 6.71e-1 AY.85
V8624 33C>T synonymous_variant S V11V 6.71e-1 AY.85
V9580 105G>A synonymous_variant N A35A 8.94e-1 AY.85
V3528 42G>T missense_variant S Q14H 7.07e-1 AY.92
V4692 212C>T missense_variant E P71L 6.70e-1 AY.95
V8885 1980T>C synonymous_variant S Y660Y 6.32e-1 AY.95
V2968 17526G>T missense_variant ORF1ab_pp1ab Q5842H 7.48e-1 AY.98.1
V4730 67G>T missense_variant M V23L 7.55e-1 AY.98.1
V1732 7866G>T missense_variant ORF1ab_pp1a K2622N 7.07e-1 AY.9
V1426 6087G>T missense_variant ORF1ab_pp1a K2029N 8.66e-1 B.1.1.153
V3440 20746G>T missense_variant ORF1ab_pp1ab V6916L 8.66e-1 B.1.1.153
V5991 897A>G synonymous_variant ORF1ab_pp1a R299R 1.00e+0 B.1.1.153
V6520 4743G>A synonymous_variant ORF1ab_pp1a T1581T 8.66e-1 B.1.1.153
V8152 17457G>T synonymous_variant ORF1ab_pp1ab V5819V 8.66e-1 B.1.1.153
V8419 19515A>G synonymous_variant ORF1ab_pp1ab V6505V 8.66e-1 B.1.1.153
V92 -33C>T upstream_gene_variant ORF1ab_pp1a None 8.66e-1 B.1.1.153
V631 1879G>T missense_variant ORF1ab_pp1a V627F 1.00e+0 B.1.1.198
V6689 6021C>T synonymous_variant ORF1ab_pp1a T2007T 7.06e-1 B.1.1.198
V3371 20216C>T missense_variant ORF1ab_pp1ab S6739L 8.43e-1 B.1.1.214
V614 1821G>T missense_variant ORF1ab_pp1a Q607H 8.43e-1 B.1.1.214
V2852 16738C>T missense_variant ORF1ab_pp1ab L5580F 6.06e-1 B.1.1.222
V3411 20495C>T missense_variant ORF1ab_pp1ab A6832V 7.22e-1 B.1.1.222
V3555 79G>T missense_variant S A27S 7.82e-1 B.1.1.222
V5064 7T>C missense_variant ORF8 F3L 9.17e-1 B.1.1.222
V5766 *4352G>T downstream_gene_variant S None 6.50e-1 B.1.1.222
V7729 14227C>T synonymous_variant ORF1ab_pp1ab L4743L 8.00e-1 B.1.1.222
V9007 2907T>C synonymous_variant S N969N 8.58e-1 B.1.1.222
V9182 252G>T synonymous_variant ORF3a L84L 7.69e-1 B.1.1.222
V3275 19697C>T missense_variant ORF1ab_pp1ab T6566M 7.07e-1 B.1.1.25
V4364 115G>A missense_variant ORF3a A39T 1.00e+0 B.1.1.25
V7258 10482C>T synonymous_variant ORF1ab_pp1a N3494N 1.00e+0 B.1.1.25
V2298 11902G>T missense_variant ORF1ab_pp1a V3968F 7.50e-1 B.1.1.28
V2875 16871C>T missense_variant ORF1ab_pp1ab P5624L 8.66e-1 B.1.1.28
V8744 870C>T synonymous_variant S D290D 7.50e-1 B.1.1.28
V8761 1029C>T synonymous_variant S N343N 8.94e-1 B.1.1.306
V5862 138T>C synonymous_variant ORF1ab_pp1a L46L 7.07e-1 B.1.1.311
V5990 885C>T synonymous_variant ORF1ab_pp1a G295G 1.00e+0 B.1.1.311
V8181 17652A>G synonymous_variant ORF1ab_pp1ab R5884R 7.07e-1 B.1.1.311
V1954 9446C>T missense_variant ORF1ab_pp1a S3149F 1.00e+0 B.1.1.326
V8658 231G>A synonymous_variant S K77K 1.00e+0 B.1.1.326
V9702 726A>G synonymous_variant N Q242Q 1.00e+0 B.1.1.326
V9763 981G>A synonymous_variant N S327S 1.00e+0 B.1.1.326
V2653 14762C>T missense_variant ORF1ab_pp1ab A4921V 6.11e-1 B.1.1.33
V2888 16929G>T missense_variant ORF1ab_pp1ab E5643D 6.54e-1 B.1.1.33
V4371 124C>T missense_variant ORF3a P42S 7.06e-1 B.1.1.33
V5844 75C>T synonymous_variant ORF1ab_pp1a D25D 6.45e-1 B.1.1.33
V6729 6273C>T synonymous_variant ORF1ab_pp1a G2091G 7.06e-1 B.1.1.33
V6942 8046C>T synonymous_variant ORF1ab_pp1a N2682N 7.06e-1 B.1.1.33
V7253 10449C>T synonymous_variant ORF1ab_pp1a L3483L 6.54e-1 B.1.1.33
V7925 15696C>T synonymous_variant ORF1ab_pp1ab A5232A 6.61e-1 B.1.1.33
V8141 17385C>T synonymous_variant ORF1ab_pp1ab C5795C 7.06e-1 B.1.1.33
V8624 33C>T synonymous_variant S V11V 6.11e-1 B.1.1.33
V9222 607T>C synonymous_variant ORF3a L203L 7.06e-1 B.1.1.33
V9551 315T>C synonymous_variant ORF8 Y105Y 7.06e-1 B.1.1.33
V3229 19346C>T missense_variant ORF1ab_pp1ab T6449I 7.07e-1 B.1.1.348
V3426 20672C>T missense_variant ORF1ab_pp1ab T6891M 7.07e-1 B.1.1.348
V4658 -15G>T upstream_gene_variant E None 7.07e-1 B.1.1.348
V9823 30G>A synonymous_variant ORF10 P10P 7.07e-1 B.1.1.348
V1134 4134G>T missense_variant ORF1ab_pp1a M1378I 7.07e-1 B.1.1.420
V1459 6184C>T missense_variant ORF1ab_pp1a L2062F 6.39e-1 B.1.1.432
V1585 6772G>T missense_variant ORF1ab_pp1a G2258C 6.34e-1 B.1.1.432
V1733 7874C>T missense_variant ORF1ab_pp1a S2625F 6.52e-1 B.1.1.432
V3435 20731G>T missense_variant ORF1ab_pp1ab G6911C 6.40e-1 B.1.1.432
V3484 21040C>A missense_variant ORF1ab_pp1ab R7014S 6.28e-1 B.1.1.432
V3486 21041G>A missense_variant ORF1ab_pp1ab R7014H 6.28e-1 B.1.1.432
V4131 2806G>T missense_variant S D936Y 6.33e-1 B.1.1.432
V6877 7569C>T synonymous_variant ORF1ab_pp1a N2523N 6.14e-1 B.1.1.432
V7401 11691C>T synonymous_variant ORF1ab_pp1a D3897D 6.38e-1 B.1.1.432
V7505 12519C>T synonymous_variant ORF1ab_pp1a N4173N 9.66e-1 B.1.1.432
V8663 250C>T synonymous_variant S L84L 6.45e-1 B.1.1.432
V918 3085A>G missense_variant ORF1ab_pp1a S1029G 6.59e-1 B.1.1.432
V4413 179C>T missense_variant ORF3a S60F 8.48e-1 B.1.1.519
V8303 18550C>T synonymous_variant ORF1ab_pp1ab L6184L 8.81e-1 B.1.1.519
V9128 3774A>G synonymous_variant S E1258E 9.05e-1 B.1.1.519
V1696 7689G>T missense_variant ORF1ab_pp1a Q2563H 9.35e-1 B.1.1.63
V2102 10738C>T missense_variant ORF1ab_pp1a H3580Y 8.45e-1 B.1.1.63
V3967 1839G>T missense_variant S Q613H 6.28e-1 B.1.1.63
V6983 8403C>T synonymous_variant ORF1ab_pp1a D2801D 7.71e-1 B.1.1.63
V7220 10185C>T synonymous_variant ORF1ab_pp1a P3395P 7.71e-1 B.1.1.63
V7264 10524C>T synonymous_variant ORF1ab_pp1a D3508D 6.28e-1 B.1.1.63
V8390 19212A>G synonymous_variant ORF1ab_pp1ab L6404L 8.45e-1 B.1.1.63
V8799 1296C>T synonymous_variant S C432C 8.45e-1 B.1.1.63
V3894 1424C>T missense_variant S A475V 1.00e+0 B.1.1.70
V2163 11023_11031delTCTGGTTTT conservative_inframe_deletion ORF1ab_pp1a S3675_F3677del 1.00e+0 B.1.177.44
V4011 2025G>T missense_variant S Q675H 1.00e+0 B.1.177.44
V5102 89C>T missense_variant ORF8 P30L 1.00e+0 B.1.177.44
V5171 218A>G missense_variant ORF8 Y73C 1.00e+0 B.1.177.44
V5237 1delA frameshift_variant&start_lost N M1fs 1.00e+0 B.1.177.44
V5248 7G>C missense_variant N D3H 1.00e+0 B.1.177.44
V5250 8A>T missense_variant N D3V 1.00e+0 B.1.177.44
V5251 9T>A missense_variant N D3E 1.00e+0 B.1.177.44
V5446 584G>T missense_variant N R195I 1.00e+0 B.1.177.44
V8012 16386C>T synonymous_variant ORF1ab_pp1ab L5462L 1.00e+0 B.1.177.44
V5776 *4358G>A downstream_gene_variant S None 7.68e-1 B.1.177.4
V9248 759C>T synonymous_variant ORF3a S253S 8.16e-1 B.1.177.75
V6176 2184C>T synonymous_variant ORF1ab_pp1a G728G 8.99e-1 B.1.177.83
V7181 9873C>T synonymous_variant ORF1ab_pp1a N3291N 9.89e-1 B.1.177.83
V7974 16113G>T synonymous_variant ORF1ab_pp1ab P5371P 8.57e-1 B.1.177.83
V1864 8674G>T missense_variant ORF1ab_pp1a V2892F 1.00e+0 B.1.398
V3540 62G>T missense_variant S R21I 7.06e-1 B.1.398
V418 1082C>T missense_variant ORF1ab_pp1a P361L 1.00e+0 B.1.400
V5587 1042G>C missense_variant N D348H 1.00e+0 B.1.400
V7792 14649C>T synonymous_variant ORF1ab_pp1ab N4883N 7.07e-1 B.1.400
V3211 19138C>T missense_variant ORF1ab_pp1ab H6380Y 8.16e-1 B.1.470
V6716 6156G>T synonymous_variant ORF1ab_pp1a V2052V 1.00e+0 B.1.470
V4893 116C>T missense_variant ORF7a T39I 6.87e-1 B.1.526
V6630 5547C>T synonymous_variant ORF1ab_pp1a D1849D 6.13e-1 B.1.526
V6878 7575C>T synonymous_variant ORF1ab_pp1a D2525D 8.25e-1 B.1.526
V4045 2111C>T missense_variant S S704L 7.07e-1 B.1.560
V862 2911C>T missense_variant ORF1ab_pp1a P971S 7.07e-1 B.1.560
V4842 -5C>T upstream_gene_variant ORF7a None 1.00e+0 B.1.588
V7786 14589T>C synonymous_variant ORF1ab_pp1ab F4863F 1.00e+0 B.1.588
V7241 10350C>T synonymous_variant ORF1ab_pp1a D3450D 7.07e-1 B.1.595
V55 -78G>A upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.596
V4609 718C>T missense_variant ORF3a P240S 6.66e-1 B.1.617.1
V147 133C>T missense_variant ORF1ab_pp1a H45Y 7.07e-1 B.1.621.1
V2533 13711G>T missense_variant ORF1ab_pp1ab G4571C 1.00e+0 B.1.621.1
V4457 286C>T missense_variant ORF3a L96F 1.00e+0 B.1.621.1
V4649 806C>T missense_variant ORF3a T269M 1.00e+0 B.1.621.1
V808 2680G>A missense_variant ORF1ab_pp1a G894S 7.07e-1 B.1.621.1
V8300 18540C>T synonymous_variant ORF1ab_pp1ab S6180S 1.00e+0 B.1.621.1
V8636 129C>T synonymous_variant S F43F 1.00e+0 B.1.621.1
V2325 12145A>G missense_variant ORF1ab_pp1a I4049V 7.07e-1 BA.1.1.15
V8496 20172C>T synonymous_variant ORF1ab_pp1ab D6724D 7.50e-1 BA.1.14.1
V6638 5619C>T synonymous_variant ORF1ab_pp1a Y1873Y 1.00e+0 BA.2.3.11
V8285 18429C>T synonymous_variant ORF1ab_pp1ab S6143S 8.16e-1 BA.2.3.11
V5401 464C>T missense_variant N A155V 7.07e-1 BA.2.65
V3604 268G>A missense_variant S V90I 1.00e+0 BA.2.73
V5730 *4316A>G downstream_gene_variant S None 1.00e+0 BA.2.73
V7970 16098C>T synonymous_variant ORF1ab_pp1ab V5366V 1.00e+0 BA.2.73
V9314 213C>T synonymous_variant M Y71Y 1.00e+0 BA.2.73
V677 2041C>T missense_variant ORF1ab_pp1a L681F 8.96e-1 BA.2.75.2
V6954 8109A>G synonymous_variant ORF1ab_pp1a V2703V 9.57e-1 BA.2.75.2
V8812 1431C>T synonymous_variant S S477S 1.00e+0 BA.4.1.9
V4432 217C>T missense_variant ORF3a L73F 7.07e-1 BA.4.6.5
V7416 11778C>T synonymous_variant ORF1ab_pp1a D3926D 1.00e+0 BA.4.7
V7722 14166G>T synonymous_variant ORF1ab_pp1ab V4722V 7.07e-1 BA.4
V1284 5078C>T missense_variant ORF1ab_pp1a P1693L 1.00e+0 BA.5.1.12
V5013 10C>T missense_variant ORF7b L4F 1.00e+0 BA.5.1.12
V731 2309C>T missense_variant ORF1ab_pp1a T770I 8.16e-1 BA.5.1.12
V1284 5078C>T missense_variant ORF1ab_pp1a P1693L 1.00e+0 BA.5.1.15
V7744 14335C>T synonymous_variant ORF1ab_pp1ab L4779L 1.00e+0 BA.5.1.15
V9227 630C>T synonymous_variant ORF3a D210D 1.00e+0 BA.5.1.15
V1284 5078C>T missense_variant ORF1ab_pp1a P1693L 1.00e+0 BA.5.1.17
V6833 7155C>T synonymous_variant ORF1ab_pp1a I2385I 1.00e+0 BA.5.1.17
V2958 17470C>T missense_variant ORF1ab_pp1ab L5824F 8.66e-1 BA.5.1.22
V7501 12504G>A synonymous_variant ORF1ab_pp1a A4168A 7.07e-1 BA.5.1.25
V372 913C>T missense_variant ORF1ab_pp1a P305S 1.00e+0 BA.5.1.2
V171 224A>G missense_variant ORF1ab_pp1a D75G 7.07e-1 BA.5.1.30
V2416 12854C>T missense_variant ORF1ab_pp1a A4285V 1.00e+0 BA.5.1.30
V9368 480C>T synonymous_variant M D160D 1.00e+0 BA.5.1.30
V2375 12524C>T missense_variant ORF1ab_pp1a T4175I 7.74e-1 BA.5.2.2
V3215 19195A>G missense_variant ORF1ab_pp1ab I6399V 1.00e+0 BA.5.2.2
V3773 752C>T missense_variant S P251L 1.00e+0 BA.5.2.43
V2357 12439G>A missense_variant ORF1ab_pp1a V4147I 8.94e-1 BA.5.2.6
V3373 20223G>T missense_variant ORF1ab_pp1ab K6741N 7.56e-1 BA.5.2.6
V7941 15828C>T synonymous_variant ORF1ab_pp1ab Y5276Y 7.56e-1 BA.5.2.6
V5410 497C>T missense_variant N T166I 7.07e-1 BA.5.3
V8132 17286C>T synonymous_variant ORF1ab_pp1ab L5762L 8.45e-1 BN.1.3.1
V9438 120C>T synonymous_variant ORF7a Y40Y 9.13e-1 BN.1.3.1
V5628 1148C>T missense_variant N P383L 1.00e+0 BQ.1.1.10
V3327 20011G>T missense_variant ORF1ab_pp1ab D6671Y 7.07e-1 BQ.1.1.18
V1416 6053C>T missense_variant ORF1ab_pp1a P2018L 1.00e+0 BQ.1.1.1
V4955 251C>T missense_variant ORF7a P84L 1.00e+0 BQ.1.1.24
V8101 17070G>T synonymous_variant ORF1ab_pp1ab T5690T 1.00e+0 BQ.1.1.24
V7611 13284C>T synonymous_variant ORF1ab_pp1ab D4428D 7.75e-1 BQ.1.1.32
V2216 11272A>G missense_variant ORF1ab_pp1a I3758V 6.31e-1 BQ.1.26.1
V4862 35T>C missense_variant ORF7a L12P 1.00e+0 BQ.1.26.1
V7340 11259T>C synonymous_variant ORF1ab_pp1a F3753F 1.00e+0 BQ.1.26.1
V1748 7975C>T missense_variant ORF1ab_pp1a H2659Y 1.00e+0 BQ.1.5
V8717 651T>C synonymous_variant S P217P 1.00e+0 BQ.1
V2849 16721C>T missense_variant ORF1ab_pp1ab T5574I 1.00e+0 BY.1
V6954 8109A>G synonymous_variant ORF1ab_pp1a V2703V 7.07e-1 BY.1
V7097 9255C>T synonymous_variant ORF1ab_pp1a F3085F 1.00e+0 BY.1
V1097 3815G>T missense_variant ORF1ab_pp1a S1272I 7.54e-1 C.16
V234 349G>T missense_variant ORF1ab_pp1a A117S 1.00e+0 C.16
V2400 12659C>T missense_variant ORF1ab_pp1a P4220L 9.65e-1 C.16
V2791 16210A>G missense_variant ORF1ab_pp1ab S5404G 1.00e+0 C.16
V4409 175G>A missense_variant ORF3a A59T 1.00e+0 C.16
V5066 8T>G missense_variant ORF8 F3C 7.42e-1 C.16
V5955 655C>T synonymous_variant ORF1ab_pp1a L219L 1.00e+0 C.16
V6395 3819C>T synonymous_variant ORF1ab_pp1a D1273D 7.42e-1 C.16
V7036 8814A>G synonymous_variant ORF1ab_pp1a V2938V 8.96e-1 C.16
V9156 117C>T synonymous_variant ORF3a A39A 1.00e+0 C.16
V5730 *4316A>G downstream_gene_variant S None 7.07e-1 C.35
V1574 6725C>T missense_variant ORF1ab_pp1a S2242F 1.00e+0 C.36.3
V4537 514G>T missense_variant ORF3a G172C 1.00e+0 C.36.3
V5002 361G>T stop_gained ORF7a E121* 7.07e-1 C.36.3
V5744 *4333G>A downstream_gene_variant S None 1.00e+0 C.36.3
V677 2041C>T missense_variant ORF1ab_pp1a L681F 1.00e+0 CA.3
V6954 8109A>G synonymous_variant ORF1ab_pp1a V2703V 1.00e+0 CA.3
V3773 752C>T missense_variant S P251L 6.85e-1 CK.1
V292 545A>G missense_variant ORF1ab_pp1a Y182C 8.16e-1 CK.3
V2929 17264C>T missense_variant ORF1ab_pp1ab T5755I 8.16e-1 CK.3
V4013 2030A>G missense_variant S Q677R 1.00e+0 CK.3
V2827 16579G>T missense_variant ORF1ab_pp1ab G5527C 7.07e-1 CN.1
V5144 184G>T missense_variant ORF8 V62L 7.07e-1 CN.1
V9652 462T>C synonymous_variant N N154N 1.00e+0 CN.1
V4362 113A>G missense_variant ORF3a Q38R 7.07e-1 P.1.7
V5927 486C>T synonymous_variant ORF1ab_pp1a N162N 7.07e-1 P.1.7
V7653 13698A>G synonymous_variant ORF1ab_pp1ab V4566V 7.07e-1 P.1.7
V7836 15015C>T synonymous_variant ORF1ab_pp1ab H5005H 7.07e-1 P.1.7
V8518 20406G>A synonymous_variant ORF1ab_pp1ab A6802A 7.07e-1 P.1.7
V9400 46C>T synonymous_variant ORF6 L16L 6.32e-1 P.2
V565 1654C>T missense_variant ORF1ab_pp1a L552F 7.07e-1 Q.3
V7427 11850C>T synonymous_variant ORF1ab_pp1a S3950S 1.00e+0 Q.3
V81 -47G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 Q.3
V7161 9723C>T synonymous_variant ORF1ab_pp1a F3241F 1.00e+0 XAZ
V1987 9838A>G missense_variant ORF1ab_pp1a M3280V 7.07e-1 XBB.1.9.1
V8836 1629C>T synonymous_variant S F543F 1.00e+0 AY.19
V9208 444C>T synonymous_variant ORF3a C148C 1.00e+0 AY.19
V4087 2452A>G missense_variant S I818V 1.00e+0 AY.21
V1579 6746C>T missense_variant ORF1ab_pp1a A2249V 1.00e+0 AY.56
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F 1.00e+0 AY.56
V2346 12300G>T missense_variant ORF1ab_pp1a Q4100H 1.00e+0 AY.56
V3470 20940G>T missense_variant ORF1ab_pp1ab K6980N 1.00e+0 AY.56
V3747 662C>T missense_variant S S221L 1.00e+0 AY.56
V5096 79C>T stop_gained ORF8 Q27* 1.00e+0 AY.56
V7889 15456C>T synonymous_variant ORF1ab_pp1ab D5152D 1.00e+0 AY.56
V9694 667C>T synonymous_variant N L223L 1.00e+0 AY.56
V1796 8332C>T missense_variant ORF1ab_pp1a L2778F 7.06e-1 B.1.1.135
V4791 625G>T missense_variant M D209Y 7.06e-1 B.1.1.135
V6026 1155C>T synonymous_variant ORF1ab_pp1a A385A 1.00e+0 B.1.1.135
V6440 4158C>T synonymous_variant ORF1ab_pp1a R1386R 1.00e+0 B.1.1.135
V4692 212C>T missense_variant E P71L 1.00e+0 B.1.1.241
V5223 358T>C missense_variant ORF8 F120L 1.00e+0 B.1.1.241
V8772 1113C>T synonymous_variant S S371S 1.00e+0 B.1.1.241
V4317 48G>T missense_variant ORF3a K16N 1.00e+0 B.1.1.27
V5446 584G>T missense_variant N R195I 7.05e-1 B.1.1.27
V5960 669C>T synonymous_variant ORF1ab_pp1a D223D 7.05e-1 B.1.1.27
V6367 3552C>T synonymous_variant ORF1ab_pp1a D1184D 7.05e-1 B.1.1.27
V6676 5931C>T synonymous_variant ORF1ab_pp1a P1977P 1.00e+0 B.1.1.27
V7824 14916C>T synonymous_variant ORF1ab_pp1ab A4972A 1.00e+0 B.1.1.27
V7874 15324C>T synonymous_variant ORF1ab_pp1ab A5108A 1.00e+0 B.1.1.27
V8047 16690C>T synonymous_variant ORF1ab_pp1ab L5564L 1.00e+0 B.1.1.27
V8267 18306C>T synonymous_variant ORF1ab_pp1ab L6102L 7.05e-1 B.1.1.27
V8474 20004A>G synonymous_variant ORF1ab_pp1ab L6668L 7.05e-1 B.1.1.27
V9495 51G>T synonymous_variant ORF7b L17L 1.00e+0 B.1.1.27
V1951 9428C>T missense_variant ORF1ab_pp1a A3143V 1.00e+0 B.1.1.322
V2873 16858G>T missense_variant ORF1ab_pp1ab A5620S 1.00e+0 B.1.1.322
V4434 225G>T missense_variant ORF3a K75N 1.00e+0 B.1.1.322
V5757 *4348C>T downstream_gene_variant S None 1.00e+0 B.1.1.322
V1300 5261C>T missense_variant ORF1ab_pp1a T1754I 1.00e+0 B.1.1.526
V1567 6629G>T missense_variant ORF1ab_pp1a C2210F 1.00e+0 B.1.1.526
V1907 9079C>T missense_variant ORF1ab_pp1a L3027F 1.00e+0 B.1.1.526
V4655 -18G>T upstream_gene_variant E None 1.00e+0 B.1.1.526
V9590 126C>T synonymous_variant N P42P 1.00e+0 B.1.1.526
V7870 15282C>T synonymous_variant ORF1ab_pp1ab A5094A 9.59e-1 B.1.160.28
V371 905C>T missense_variant ORF1ab_pp1a S302F 1.00e+0 B.1.177.31
V4011 2025G>T missense_variant S Q675H 6.96e-1 B.1.177.31
V5446 584G>T missense_variant N R195I 1.00e+0 B.1.177.31
V6542 4905C>T synonymous_variant ORF1ab_pp1a Y1635Y 1.00e+0 B.1.177.31
V1406 6020C>T missense_variant ORF1ab_pp1a T2007I 7.04e-1 B.1.179
V1459 6184C>T missense_variant ORF1ab_pp1a L2062F 8.64e-1 B.1.179
V1585 6772G>T missense_variant ORF1ab_pp1a G2258C 7.04e-1 B.1.179
V1733 7874C>T missense_variant ORF1ab_pp1a S2625F 8.64e-1 B.1.179
V2513 13598C>T missense_variant ORF1ab_pp1ab T4533I 1.00e+0 B.1.179
V2942 17351A>G missense_variant ORF1ab_pp1ab K5784R 7.04e-1 B.1.179
V3435 20731G>T missense_variant ORF1ab_pp1ab G6911C 8.64e-1 B.1.179
V3484 21040C>A missense_variant ORF1ab_pp1ab R7014S 8.64e-1 B.1.179
V3486 21041G>A missense_variant ORF1ab_pp1ab R7014H 8.64e-1 B.1.179
V3542 65C>T missense_variant S T22I 7.04e-1 B.1.179
V3777 757G>A missense_variant S D253N 7.04e-1 B.1.179
V4131 2806G>T missense_variant S D936Y 7.04e-1 B.1.179
V439 1172C>T missense_variant ORF1ab_pp1a S391F 8.64e-1 B.1.179
V4433 221C>T missense_variant ORF3a S74F 7.46e-1 B.1.179
V4598 670G>T missense_variant ORF3a G224C 8.64e-1 B.1.179
V6781 6720A>T synonymous_variant ORF1ab_pp1a L2240L 8.64e-1 B.1.179
V7073 9054C>T synonymous_variant ORF1ab_pp1a F3018F 7.04e-1 B.1.179
V7401 11691C>T synonymous_variant ORF1ab_pp1a D3897D 8.64e-1 B.1.179
V7467 12147C>T synonymous_variant ORF1ab_pp1a I4049I 7.04e-1 B.1.179
V7505 12519C>T synonymous_variant ORF1ab_pp1a N4173N 7.04e-1 B.1.179
V7703 14049T>C synonymous_variant ORF1ab_pp1ab D4683D 1.00e+0 B.1.179
V8663 250C>T synonymous_variant S L84L 7.04e-1 B.1.179
V918 3085A>G missense_variant ORF1ab_pp1a S1029G 8.64e-1 B.1.179
V9455 210C>T synonymous_variant ORF7a G70G 7.04e-1 B.1.179
V9778 1044T>C synonymous_variant N D348D 8.93e-1 B.1.179
V240 360G>T missense_variant ORF1ab_pp1a K120N 7.06e-1 B.1.332
V6774 6676C>T synonymous_variant ORF1ab_pp1a L2226L 1.00e+0 B.1.332
V707 2204C>T missense_variant ORF1ab_pp1a A735V 1.00e+0 B.1.332
V1283 5074C>T missense_variant ORF1ab_pp1a P1692S 9.55e-1 B.1.39
V3163 18808G>T missense_variant ORF1ab_pp1ab D6270Y 7.31e-1 B.1.39
V6178 2190C>T synonymous_variant ORF1ab_pp1a L730L 6.74e-1 B.1.39
V6817 7002C>T synonymous_variant ORF1ab_pp1a F2334F 1.00e+0 B.1.39
V820 2762A>G missense_variant ORF1ab_pp1a Y921C 1.00e+0 B.1.39
V3002 17822C>T missense_variant ORF1ab_pp1ab T5941I 1.00e+0 B.1.405
V5736 *4322G>C downstream_gene_variant S None 1.00e+0 B.1.405
V8521 20415G>T synonymous_variant ORF1ab_pp1ab P6805P 1.00e+0 B.1.405
V9357 429G>C synonymous_variant M V143V 1.00e+0 B.1.405
V9519 102T>C synonymous_variant ORF8 D34D 1.00e+0 B.1.405
V5614 1129G>T missense_variant N D377Y 8.61e-1 B.1.450
V5908 378C>T synonymous_variant ORF1ab_pp1a N126N 8.61e-1 B.1.450
V6815 6990A>G synonymous_variant ORF1ab_pp1a A2330A 8.61e-1 B.1.450
V5421 539G>A missense_variant N S180N 1.00e+0 B.1.505
V3326 20010G>T missense_variant ORF1ab_pp1ab M6670I 8.61e-1 B.1.538
V8761 1029C>T synonymous_variant S N343N 1.00e+0 B.1.538
V123 70C>T missense_variant ORF1ab_pp1a R24C 1.00e+0 B.1.625
V1306 5289G>T missense_variant ORF1ab_pp1a K1763N 1.00e+0 B.1.625
V1442 6137C>T missense_variant ORF1ab_pp1a P2046L 7.06e-1 B.1.625
V3413 20498C>T missense_variant ORF1ab_pp1ab T6833I 1.00e+0 B.1.625
V4014 2031G>C missense_variant S Q677H 1.00e+0 B.1.625
V4840 181G>T missense_variant ORF6 D61Y 1.00e+0 B.1.625
V5437 572G>T missense_variant N R191L 1.00e+0 B.1.625
V7808 14766T>C synonymous_variant ORF1ab_pp1ab Y4922Y 1.00e+0 B.1.625
V9090 3513C>T synonymous_variant S G1171G 1.00e+0 B.1.625
V2638 14593G>T missense_variant ORF1ab_pp1ab V4865F 1.00e+0 B.1.9.5
V2983 17700G>T missense_variant ORF1ab_pp1ab M5900I 1.00e+0 B.1.9.5
V5129 152C>T missense_variant ORF8 A51V 1.00e+0 B.1.9.5
V5493 640G>T missense_variant N G214C 1.00e+0 B.1.9.5
V7751 14358G>T synonymous_variant ORF1ab_pp1ab T4786T 1.00e+0 B.1.9.5
V8747 888C>T synonymous_variant S L296L 7.05e-1 B.1.9.5
V8901 2049G>T synonymous_variant S R683R 1.00e+0 B.1.9.5
V1866 8699C>T missense_variant ORF1ab_pp1a S2900L 7.05e-1 CP.5
V2371 12491C>T missense_variant ORF1ab_pp1a T4164I 7.04e-1 CP.5
V545 1606T>C missense_variant ORF1ab_pp1a F536L 1.00e+0 CP.5
V5985 837C>T synonymous_variant ORF1ab_pp1a S279S 7.05e-1 CP.5
V5627 1147C>T missense_variant N P383S 1.00e+0 L.2





Manual curation of mutation (2857G>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