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The current mutation

ID: V1574
DNA: 6725C>T
Protein: S2242F
Position: 6990








COV2Var annotation categories







Summary information of mutation (6725C>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   6990
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 6725C>T
  Ref Seq: C
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: S2242F
  Protein 3-letter Mutation: Ser2242Phe

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 (6725C>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.1 268 91 3.40e-1
2020-10 B.1.1.25 268 65 2.43e-1
2020-10 B.1.1.416 268 65 2.43e-1
2020-11 B.1.1.416 319 133 4.17e-1
2020-11 B.1.1.25 319 61 1.91e-1
2020-11 B.1 319 47 1.47e-1
2020-12 B.1.1.416 824 414 5.02e-1
2020-12 B.1.1.25 824 156 1.89e-1
2020-12 B.1.1 824 54 6.55e-2
2020-03 B.29 129 61 4.73e-1
2020-03 B.1.395 129 37 2.87e-1
2020-03 B.1.35 129 19 1.47e-1
2020-04 B.1.35 174 72 4.14e-1
2020-04 B.1.395 174 38 2.18e-1
2020-04 B.29 174 31 1.78e-1
2020-05 B.1.35 55 18 3.27e-1
2020-05 B.1 55 13 2.36e-1
2020-05 B.1.395 55 5 9.09e-2
2020-06 B.1 26 8 3.08e-1
2020-06 B.1.1 26 6 2.31e-1
2020-06 B.1.206 26 3 1.15e-1
2020-07 B.1.1.284 163 100 6.13e-1
2020-07 B.1 163 36 2.21e-1
2020-07 B.1.2 163 6 3.68e-2
2020-08 B.1.1.284 459 358 7.80e-1
2020-08 B.1 459 63 1.37e-1
2020-08 B.1.1.521 459 6 1.31e-2
2020-09 B.1 214 100 4.67e-1
2020-09 B.1.1.284 214 51 2.38e-1
2020-09 B.1.139 214 26 1.21e-1
2021-01 B.1.1.416 1027 345 3.36e-1
2021-01 B.1.1.25 1027 252 2.45e-1
2021-01 B.1.1 1027 94 9.15e-2
2021-10 AY.4 1249 384 3.07e-1
2021-10 AY.120 1249 144 1.15e-1
2021-10 AY.3.3 1249 87 6.97e-2
2021-11 AY.4 1656 309 1.87e-1
2021-11 AY.3.3 1656 188 1.14e-1
2021-11 AY.120 1656 170 1.03e-1
2021-12 AY.3.3 1624 246 1.51e-1
2021-12 AY.4 1624 244 1.50e-1
2021-12 AY.120 1624 184 1.13e-1
2021-02 B.1.1.416 624 132 2.12e-1
2021-02 B.1.1.7 624 115 1.84e-1
2021-02 B.1.427 624 58 9.29e-2
2021-03 B.1.1.7 726 340 4.68e-1
2021-03 B.1.427 726 152 2.09e-1
2021-03 B.1.2 726 37 5.10e-2
2021-04 B.1.1.7 603 398 6.60e-1
2021-04 B.1.427 603 78 1.29e-1
2021-04 B.1.526 603 17 2.82e-2
2021-05 B.1.1.7 449 319 7.10e-1
2021-05 B.1.351.2 449 21 4.68e-2
2021-05 P.1 449 13 2.90e-2
2021-06 B.1.1.7 420 116 2.76e-1
2021-06 AY.4 420 87 2.07e-1
2021-06 AY.24 420 42 1.00e-1
2021-07 AY.4 861 398 4.62e-1
2021-07 AY.24 861 74 8.59e-2
2021-07 B.1.1.7 861 67 7.78e-2
2021-08 AY.4 1095 351 3.21e-1
2021-08 AY.44 1095 96 8.77e-2
2021-08 B.1.617.2 1095 87 7.95e-2
2021-09 AY.4 1006 375 3.73e-1
2021-09 AY.25.1 1006 85 8.45e-2
2021-09 AY.44 1006 75 7.46e-2
2022-01 BA.1 690 160 2.32e-1
2022-01 BA.1.1 690 159 2.30e-1
2022-01 BA.1.18 690 48 6.96e-2
2022-10 BA.4.6.4 399 123 3.08e-1
2022-10 BF.7 399 47 1.18e-1
2022-10 BF.5 399 17 4.26e-2
2022-11 BQ.1 374 54 1.44e-1
2022-11 BF.7 374 41 1.10e-1
2022-11 BA.4.6.4 374 38 1.02e-1
2022-12 BQ.1 417 87 2.09e-1
2022-12 BQ.1.1 417 47 1.13e-1
2022-12 BF.7 417 34 8.15e-2
2022-02 BA.1.1 744 287 3.86e-1
2022-02 BA.2 744 84 1.13e-1
2022-02 BA.1 744 83 1.12e-1
2022-03 BA.2 737 447 6.07e-1
2022-03 BA.1.1 737 130 1.76e-1
2022-03 BA.2.9 737 36 4.88e-2
2022-04 BA.2 553 418 7.56e-1
2022-04 BA.2.9 553 46 8.32e-2
2022-04 BA.1.1 553 20 3.62e-2
2022-05 BA.2 378 262 6.93e-1
2022-05 BA.2.9 378 34 8.99e-2
2022-05 BA.5.5 378 21 5.56e-2
2022-06 BA.2 314 92 2.93e-1
2022-06 BA.5.5 314 92 2.93e-1
2022-06 BA.4.6.4 314 14 4.46e-2
2022-07 BA.5.5 345 101 2.93e-1
2022-07 BA.4.6.4 345 47 1.36e-1
2022-07 BA.2 345 33 9.57e-2
2022-08 BA.4.6.4 388 127 3.27e-1
2022-08 BA.5.5 388 51 1.31e-1
2022-08 BF.5 388 29 7.47e-2
2022-09 BA.4.6.4 440 148 3.36e-1
2022-09 BF.7 440 36 8.18e-2
2022-09 BF.5 440 30 6.82e-2
2023-01 XBB.1.5 355 63 1.77e-1
2023-01 BQ.1.1 355 50 1.41e-1
2023-01 BQ.1 355 36 1.01e-1
2023-02 XBB.1.5 99 37 3.74e-1
2023-02 BQ.1.1 99 9 9.09e-2
2023-02 BE.4.2 99 4 4.04e-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
V1574 AT.1 1.74e-2 3 2021-1-18 2021-8-3
V1574 AY.108 1.16e-2 8 2021-5-12 2022-10-26
V1574 AY.120 1.88e-2 602 2020-10-26 2022-9-28
V1574 AY.24 6.73e-2 218 2021-2-12 2022-5-9
V1574 AY.3.3 5.24e-1 534 2021-7-23 2022-2-7
V1574 AY.32 1.02e-2 20 2021-4-16 2022-3-23
V1574 AY.4.11 2.06e-2 32 2021-6-17 2022-2-14
V1574 AY.43.7 6.57e-2 13 2021-8-31 2022-1-6
V1574 AY.99 1.15e-2 8 2021-4-16 2022-2-9
V1574 B.1.1.176 1.31e-2 36 2020-3-12 2021-7-6
V1574 B.1.1.189 1.12e-2 7 2020-4-11 2021-10-16
V1574 B.1.1.25 2.72e-1 561 2020-3-31 2022-8-1
V1574 B.1.1.284 5.35e-2 511 2020-5-22 2021-5-31
V1574 B.1.1.416 8.20e-1 1137 2020-3-19 2021-9-17
V1574 B.1.1.521 1.55e-2 3 2020-5-15 2021-10-23
V1574 B.1.1.57 2.25e-2 2 2020-3-31 2021-3-9
V1574 B.1.139 5.37e-2 85 2020-3-18 2021-9-14
V1574 B.1.146 1.29e-2 3 2020-6-23 2021-6-28
V1574 B.1.177.20 2.84e-2 18 2020-3-21 2021-3-31
V1574 B.1.177.81 1.46e-2 74 2020-8-10 2021-10-12
V1574 B.1.177.83 6.55e-2 40 2020-8-25 2021-6-8
V1574 B.1.177.86 1.35e-2 72 2020-9-21 2022-8-30
V1574 B.1.241 3.42e-2 52 2020-4-15 2021-12-10
V1574 B.1.35 9.65e-1 111 2020-3-20 2020-6-11
V1574 B.1.351.2 2.38e-2 84 2020-11-3 2021-10-12
V1574 B.1.36.34 7.14e-2 3 2020-6-10 2021-3-2
V1574 B.1.395 9.34e-1 113 2020-3-6 2021-8-8
V1574 B.1.427 1.51e-2 321 2020-4-11 2022-11-12
V1574 B.1.468 1.28e-2 2 2020-2-13 2021-4-15
V1574 B.1.572 3.24e-1 12 2020-4-2 2020-7-22
V1574 B.1.575 1.04e-2 33 2020-10-23 2022-5-19
V1574 B.1.621.1 3.81e-2 71 2021-4-9 2022-5-25
V1574 B.1.636 1.67e-1 18 2021-1-6 2021-7-10
V1574 B.29 3.77e-1 93 2020-2-27 2020-6-14
V1574 BA.2.72 1.42e-2 15 2022-2-13 2022-9-13
V1574 BA.2.75.6 1.11e-2 2 2022-6-16 2023-2-1
V1574 BA.4.6.4 3.05e-1 505 2022-5-29 2023-1-31
V1574 BA.5.1.19 1.99e-2 12 2022-6-5 2023-2-6
V1574 BE.4.2 1.56e-2 6 2022-9-1 2023-2-22
V1574 BF.7.10 5.47e-2 17 2022-6-27 2023-2-7
V1574 BG.2 1.36e-2 15 2022-2-26 2022-9-8
V1574 BY.1 2.74e-2 37 2022-1-1 2023-2-20
V1574 CH.1.1.5 1.86e-2 9 2022-11-9 2023-2-22
V1574 P.6 1.21e-2 3 2020-12-2 2021-4-25






Examining mutation (6725C>T) found in abundant sequences of non-human animal hosts

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

Animal host Lineage Source region Collection date Accession ID
Odocoileus virginianus B.1.234 USA 2020-12-10 EPI_ISL_5804732
Odocoileus virginianus AY.44 Canada 2021-11-7 EPI_ISL_10169675
Odocoileus virginianus AY.44 USA 2021-12-1 EPI_ISL_9347726
Odocoileus virginianus AY.44 USA 2021-12-1 EPI_ISL_16297274
Odocoileus virginianus AY.100 USA 2021-11-21 EPI_ISL_16297227
Odocoileus virginianus P.1 USA 2021-11-28 EPI_ISL_16308828
Odocoileus virginianus B.1.1.7 USA 2021-11-22 EPI_ISL_16297279
Odocoileus virginianus B.1.1.7 USA 2021-11-20 EPI_ISL_13658806
Odocoileus virginianus B.1.1.7 USA 2021-11-8 EPI_ISL_13610659
Odocoileus virginianus AY.75 USA 2021-11-10 EPI_ISL_13610666
Odocoileus virginianus B.1.1.7 USA 2021-11-20 EPI_ISL_13610686
Odocoileus virginianus B.1.1.7 USA 2021-12-4 EPI_ISL_13610694
Canis lupus familiaris B.1.1.7 Thailand 2021-5-4 EPI_ISL_2628963
Odocoileus virginianus AY.103 USA 2022-3-11 EPI_ISL_16429146




Association between mutation (6725C>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 -1.18e+0 1.11e+0 -1.06e+0 2.88e-1 Decrease
Deceased 4.24e-1 6.42e-1 6.61e-1 5.09e-1 Increase
Homebound -1.86e+1 1.04e+4 -1.79e-3 9.99e-1 Decrease
Hospitalized -2.27e-1 3.73e-1 -6.09e-1 5.42e-1 Decrease
Mild -2.24e+0 1.03e+0 -2.18e+0 2.96e-2 Decrease
Recovered 1.43e+0 3.84e-1 3.73e+0 1.90e-4 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 -5.63e-2 7.95e-2 -7.08e-1 4.79e-1 Decrease
18-39 -1.76e-1 4.46e-2 -3.94e+0 8.17e-5 Decrease
40-64 1.88e-2 4.44e-2 4.23e-1 6.73e-1 Increase
65-84 1.52e-1 6.30e-2 2.41e+0 1.59e-2 Increase
>=85 6.02e-1 9.62e-2 6.26e+0 3.95e-10 Increase

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

Attribute Effect Estimate SE Z-value P-value Direction
Patient gender Male 8.18e-3 4.29e-2 1.90e-1 8.49e-1 Increase





Investigating natural selection at mutation (6725C>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 1424 0.00e+0 BE.10 MEME
nsp3 2720 8554 1945 1424 3.00e-2 BQ.1.8 MEME
nsp3 2720 8554 1945 1424 3.00e-2 AY.25.2 MEME
nsp3 2720 8554 1945 1424 0.00e+0 B.1.526 MEME
nsp3 2720 8554 1945 1424 4.00e-2 B.1.617.2 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
nsp3 2720 8554 1945 1424 0.00 7.13 3.00e-2 B.1.617.2 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
nsp3 2720 8554 1945 1424 1.00e-2 9.70e-1 BA.5.3.1 FUBAR
nsp3 2720 8554 1945 1424 2.00e-2 9.50e-1 BM.1.1.1 FUBAR
nsp3 2720 8554 1945 1424 0.00e+0 9.80e-1 B.1.617.2 FUBAR




Alterations in protein physicochemical properties induced by mutation (6725C>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 490049.01 6.04 543550 88.99 -0.022
Reference ORF1ab_pp1a 489988.91 6.04 543550 88.99 -0.023




Alterations in protein stability induced by mutation (6725C>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
S2242F ORF1ab_pp1a Point 2242 -1.18 Decrease 7 25 Environment
S2242F ORF1ab_pp1a Point 2242 -1.18 Decrease 7.4 37 Internal




Impact on protein function induced by mutation (6725C>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
S2242F ORF1ab_pp1a Point 0.326 Altered Cytoplasmic_loop (Pr = 0.27 | P = 5.2e-04)
Altered PPI_hotspot (Pr = 0.24 | P = 0.03)




Exploring mutation (6725C>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 (6725C>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
S2242F ORF1ab_pp1a 6990 Chymotrypsin-high specificity CLGFLIYSTA (pos: 2242)
 NA
S2242F ORF1ab_pp1a 6990 Pepsin (pH1.3) VCLGFLIYST (pos: 2241)
 NA
S2242F ORF1ab_pp1a 6990 Proteinase K CLGFLIYSTA (pos: 2242)
 NA
S2242F ORF1ab_pp1a 6990 Thermolysin VCLGFLIYST (pos: 2241)
 NA
S2242F ORF1ab_pp1a 6990 Chymotrypsin-low specificity CLGFLIYSTA (pos: 2242)
 NA
S2242F ORF1ab_pp1a 6990 Pepsin (pH>2) VCLGFLIYST (pos: 2241)
 NA




Impact of spike protein mutation (6725C>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 (6725C>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 (6725C>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 (6725C>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
V2575 13986G>T missense_variant ORF1ab_pp1ab L4662F 8.82e-1 AY.25.1
V6821 7038C>T synonymous_variant ORF1ab_pp1a I2346I 6.56e-1 BA.5.5
V4138 2824G>T missense_variant S A942S 6.39e-1 AY.125
V4431 215C>T missense_variant ORF3a A72V 6.84e-1 AY.125
V8475 20013T>C synonymous_variant ORF1ab_pp1ab D6671D 7.26e-1 AY.26
V5418 535G>A missense_variant N G179S 6.42e-1 AY.39
V2304 11937G>T missense_variant ORF1ab_pp1a K3979N 7.08e-1 B.1.1
V4191 3310G>T missense_variant S V1104L 7.15e-1 B.1.1
V470 1286C>T missense_variant ORF1ab_pp1a A429V 8.46e-1 B.1.1
V7878 15351C>T synonymous_variant ORF1ab_pp1ab H5117H 6.23e-1 B.1.1
V941 3203G>A missense_variant ORF1ab_pp1a G1068E 8.44e-1 B.1.1
V1684 7595C>T missense_variant ORF1ab_pp1a T2532I 6.88e-1 BA.5.6
V8293 18483C>T synonymous_variant ORF1ab_pp1ab V6161V 6.22e-1 BA.5.6
V1767 8092C>T missense_variant ORF1ab_pp1a H2698Y 6.55e-1 BF.7
V724 2279C>A missense_variant ORF1ab_pp1a T760N 1.00e+0 A.2.5.2
V2402 12668C>T missense_variant ORF1ab_pp1a P4223L 6.12e-1 A
V4984 310G>T missense_variant ORF7a V104F 7.07e-1 A
V5154 196G>A missense_variant ORF8 G66S 6.32e-1 AY.105
V5184 260C>T missense_variant ORF8 T87I 7.05e-1 AY.108
V7763 14439C>T synonymous_variant ORF1ab_pp1ab D4813D 7.89e-1 AY.108
V5269 34G>T missense_variant N A12S 6.70e-1 AY.109
V5419 535G>T missense_variant N G179C 7.74e-1 AY.109
V7758 14412C>T synonymous_variant ORF1ab_pp1ab P4804P 6.70e-1 AY.109
V1680 7558C>T missense_variant ORF1ab_pp1a H2520Y 8.37e-1 AY.111
V1658 7447C>T missense_variant ORF1ab_pp1a P2483S 6.66e-1 AY.116.1
V2299 11906C>T missense_variant ORF1ab_pp1a A3969V 6.66e-1 AY.116.1
V4026 2048G>T missense_variant S R683L 6.12e-1 AY.116.1
V1169 4418C>T missense_variant ORF1ab_pp1a A1473V 8.27e-1 AY.118
V1626 7034C>T missense_variant ORF1ab_pp1a A2345V 7.73e-1 AY.118
V3076 18224T>C missense_variant ORF1ab_pp1ab I6075T 7.83e-1 AY.120
V6386 3756C>T synonymous_variant ORF1ab_pp1a N1252N 7.88e-1 AY.120
V8147 17427A>G synonymous_variant ORF1ab_pp1ab S5809S 7.75e-1 AY.120
V9827 57C>T synonymous_variant ORF10 C19C 7.39e-1 AY.120
V1247 4835C>T missense_variant ORF1ab_pp1a S1612L 8.94e-1 AY.122.5
V5897 318C>T synonymous_variant ORF1ab_pp1a V106V 1.00e+0 AY.124.1
V6425 4035G>T synonymous_variant ORF1ab_pp1a V1345V 7.33e-1 AY.127
V703 2193G>T missense_variant ORF1ab_pp1a M731I 8.91e-1 AY.127
V7830 14976C>T synonymous_variant ORF1ab_pp1ab N4992N 6.76e-1 AY.127
V8601 21042C>T synonymous_variant ORF1ab_pp1ab R7014R 7.37e-1 AY.127
V5818 *4409T>C downstream_gene_variant S None 7.81e-1 AY.129
V7307 10959C>T synonymous_variant ORF1ab_pp1a V3653V 6.25e-1 AY.129
V7452 12030C>T synonymous_variant ORF1ab_pp1a T4010T 7.41e-1 AY.129
V7617 13321C>T synonymous_variant ORF1ab_pp1ab L4441L 8.03e-1 AY.129
V1340 5519C>T missense_variant ORF1ab_pp1a T1840I 6.65e-1 AY.131
V2928 17259G>T missense_variant ORF1ab_pp1ab M5753I 8.16e-1 AY.131
V4434 225G>T missense_variant ORF3a K75N 8.16e-1 AY.131
V7464 12135C>T synonymous_variant ORF1ab_pp1a L4045L 8.16e-1 AY.131
V760 2441C>T missense_variant ORF1ab_pp1a T814I 8.16e-1 AY.131
V8359 18922C>T synonymous_variant ORF1ab_pp1ab L6308L 8.16e-1 AY.131
V909 3058G>A missense_variant ORF1ab_pp1a V1020I 8.16e-1 AY.131
V1237 4775A>G missense_variant ORF1ab_pp1a Q1592R 1.00e+0 AY.16
V19 -166C>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 AY.16
V2704 15332A>G missense_variant ORF1ab_pp1ab Y5111C 6.24e-1 AY.24
V980 3328C>T missense_variant ORF1ab_pp1a L1110F 9.78e-1 AY.24
V2550 13856C>T missense_variant ORF1ab_pp1ab P4619L 7.07e-1 AY.25.3
V4510 400C>T missense_variant ORF3a R134C 7.07e-1 AY.25.3
V4777 407G>A missense_variant M S136N 8.16e-1 AY.2
V1062 3658C>T missense_variant ORF1ab_pp1a P1220S 8.01e-1 AY.30
V1369 5761C>T missense_variant ORF1ab_pp1a P1921S 8.66e-1 AY.30
V7512 12564A>G synonymous_variant ORF1ab_pp1a L4188L 8.66e-1 AY.30
V2648 14743G>A missense_variant ORF1ab_pp1ab D4915N 6.30e-1 AY.3.3
V9830 102C>T synonymous_variant ORF10 N34N 6.92e-1 AY.3.3
V2130 10879A>G missense_variant ORF1ab_pp1a M3627V 7.07e-1 AY.36.1
V2818 16480G>A missense_variant ORF1ab_pp1ab G5494S 7.07e-1 AY.36.1
V6042 1254C>T synonymous_variant ORF1ab_pp1a N418N 7.07e-1 AY.36.1
V3100 18387G>T missense_variant ORF1ab_pp1ab E6129D 1.00e+0 AY.37
V7554 12897T>C synonymous_variant ORF1ab_pp1a C4299C 7.07e-1 AY.37
V3268 19637C>T missense_variant ORF1ab_pp1ab A6546V 7.43e-1 AY.39.1
V5541 800C>T missense_variant N A267V 9.55e-1 AY.4.11
V3493 21101C>T missense_variant ORF1ab_pp1ab P7034L 8.74e-1 AY.4.17
V3567 162G>C missense_variant S L54F 7.89e-1 AY.4.17
V5936 546C>T synonymous_variant ORF1ab_pp1a Y182Y 9.53e-1 AY.4.2.2
V138 101C>T missense_variant ORF1ab_pp1a S34F 7.07e-1 AY.42
V2745 15718G>T missense_variant ORF1ab_pp1ab V5240L 8.18e-1 AY.42
V7034 8805T>C synonymous_variant ORF1ab_pp1a D2935D 1.00e+0 AY.43.2
V4270 3707G>T missense_variant S C1236F 1.00e+0 AY.43.3
V1780 8215C>T missense_variant ORF1ab_pp1a P2739S 1.00e+0 AY.4.4
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 1.00e+0 AY.4.4
V6836 7170T>C synonymous_variant ORF1ab_pp1a F2390F 1.00e+0 AY.4.4
V1954 9446C>T missense_variant ORF1ab_pp1a S3149F 1.00e+0 AY.46.1
V3634 425_433delGTGTTTATT disruptive_inframe_deletion S G142_Y145delinsD 7.07e-1 AY.46.2
V565 1654C>T missense_variant ORF1ab_pp1a L552F 1.00e+0 AY.46.2
V5665 -15G>C upstream_gene_variant ORF10 None 7.07e-1 AY.46.2
V6183 2223C>T synonymous_variant ORF1ab_pp1a F741F 7.07e-1 AY.46.2
V7790 14634C>T synonymous_variant ORF1ab_pp1ab G4878G 1.00e+0 AY.46.2
V4608 717G>T missense_variant ORF3a E239D 7.07e-1 AY.46.4
V7230 10260C>T synonymous_variant ORF1ab_pp1a V3420V 1.00e+0 AY.46.4
V3742 644A>G missense_variant S D215G 9.72e-1 AY.4.8
V5396 451C>T missense_variant N P151S 6.42e-1 AY.4.8
V7966 16059C>T synonymous_variant ORF1ab_pp1ab C5353C 9.72e-1 AY.4.8
V8843 1686C>T synonymous_variant S F562F 8.08e-1 AY.4.8
V6227 2508C>T synonymous_variant ORF1ab_pp1a Y836Y 8.66e-1 AY.48
V5499 649G>T missense_variant N A217S 7.07e-1 AY.50
V1709 7775A>G missense_variant ORF1ab_pp1a D2592G 7.07e-1 AY.5.3
V9129 3777C>T synonymous_variant S D1259D 7.07e-1 AY.5.3
V326 671C>T missense_variant ORF1ab_pp1a T224I 7.07e-1 AY.53
V3847 1151C>T missense_variant S P384L 7.07e-1 AY.5.4
V8446 19698G>T synonymous_variant ORF1ab_pp1ab T6566T 9.26e-1 AY.61
V9446 156C>T synonymous_variant ORF7a N52N 9.13e-1 AY.61
V2193 11185C>A missense_variant ORF1ab_pp1a Q3729K 1.00e+0 AY.88
V3483 21038C>T missense_variant ORF1ab_pp1ab P7013L 1.00e+0 AY.88
V3486 21041G>A missense_variant ORF1ab_pp1ab R7014H 7.07e-1 AY.88
V4203 3371G>T missense_variant S G1124V 1.00e+0 AY.88
V7426 11835C>T synonymous_variant ORF1ab_pp1a A3945A 1.00e+0 AY.88
V760 2441C>T missense_variant ORF1ab_pp1a T814I 1.00e+0 AY.88
V7966 16059C>T synonymous_variant ORF1ab_pp1ab C5353C 1.00e+0 AY.88
V8843 1686C>T synonymous_variant S F562F 7.07e-1 AY.88
V9168 180C>A synonymous_variant ORF3a S60S 1.00e+0 AY.88
V980 3328C>T missense_variant ORF1ab_pp1a L1110F 6.03e-1 AY.98.1
V2266 11726A>G missense_variant ORF1ab_pp1a E3909G 9.35e-1 AY.99
V3897 1430G>T missense_variant S S477I 1.00e+0 AY.99
V4015 2031G>T missense_variant S Q677H 6.10e-1 AY.99
V4695 217C>T missense_variant E L73F 1.00e+0 AY.99
V4954 250C>T missense_variant ORF7a P84S 1.00e+0 AY.99
V8438 19632T>C synonymous_variant ORF1ab_pp1ab A6544A 1.00e+0 AY.99
V8679 348C>T synonymous_variant S S116S 9.35e-1 AY.99
V1018 3473C>T missense_variant ORF1ab_pp1a P1158L 7.07e-1 B.1.110.3
V55 -78G>A upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.110.3
V7099 9267C>T synonymous_variant ORF1ab_pp1a F3089F 7.07e-1 B.1.110.3
V3054 18076G>A missense_variant ORF1ab_pp1ab V6026I 6.66e-1 B.1.1.10
V3413 20498C>T missense_variant ORF1ab_pp1ab T6833I 7.74e-1 B.1.1.10
V474 1307C>T missense_variant ORF1ab_pp1a T436I 1.00e+0 B.1.1.10
V5759 *4349C>T downstream_gene_variant S None 6.11e-1 B.1.1.10
V5783 *4361G>T downstream_gene_variant S None 8.16e-1 B.1.1.10
V6183 2223C>T synonymous_variant ORF1ab_pp1a F741F 8.16e-1 B.1.1.10
V7975 16122C>T synonymous_variant ORF1ab_pp1ab C5374C 8.66e-1 B.1.1.10
V8811 1425C>T synonymous_variant S A475A 1.00e+0 B.1.1.10
V354 848C>T missense_variant ORF1ab_pp1a T283I 1.00e+0 B.1.111
V5985 837C>T synonymous_variant ORF1ab_pp1a S279S 7.07e-1 B.1.111
V8027 16542C>T synonymous_variant ORF1ab_pp1ab N5514N 6.85e-1 B.1.1.176
V1073 3690G>T missense_variant ORF1ab_pp1a K1230N 8.44e-1 B.1.1.189
V141 111G>T missense_variant ORF1ab_pp1a E37D 7.54e-1 B.1.1.189
V1491 6278C>T missense_variant ORF1ab_pp1a T2093I 9.25e-1 B.1.1.189
V2217 11275G>T missense_variant ORF1ab_pp1a V3759F 9.25e-1 B.1.1.189
V4535 512C>T missense_variant ORF3a S171L 9.25e-1 B.1.1.189
V5430 556T>C missense_variant N S186P 8.44e-1 B.1.1.189
V5790 *4367G>T downstream_gene_variant S None 9.25e-1 B.1.1.189
V6649 5709C>T synonymous_variant ORF1ab_pp1a D1903D 8.44e-1 B.1.1.189
V6818 7014C>T synonymous_variant ORF1ab_pp1a F2338F 7.54e-1 B.1.1.189
V7220 10185C>T synonymous_variant ORF1ab_pp1a P3395P 9.25e-1 B.1.1.189
V8131 17283C>T synonymous_variant ORF1ab_pp1ab F5761F 7.54e-1 B.1.1.189
V5657 1254G>T missense_variant N Q418H 6.66e-1 B.1.1.216
V6170 2151C>T synonymous_variant ORF1ab_pp1a Y717Y 8.16e-1 B.1.1.216
V864 2912C>T missense_variant ORF1ab_pp1a P971L 8.16e-1 B.1.1.216
V1343 5539T>A missense_variant ORF1ab_pp1a C1847S 9.89e-1 B.1.1.25
V4643 790T>C missense_variant ORF3a Y264H 9.89e-1 B.1.1.25
V5792 *4370C>T downstream_gene_variant S None 9.05e-1 B.1.1.25
V633 1886A>G missense_variant ORF1ab_pp1a D629G 9.89e-1 B.1.1.25
V8113 17163G>T synonymous_variant ORF1ab_pp1ab V5721V 9.83e-1 B.1.1.25
V8562 20784T>C synonymous_variant ORF1ab_pp1ab D6928D 9.90e-1 B.1.1.25
V2761 15914C>T missense_variant ORF1ab_pp1ab S5305L 1.00e+0 B.1.1.277
V2795 16264G>T missense_variant ORF1ab_pp1ab V5422F 1.00e+0 B.1.1.277
V4382 134G>T missense_variant ORF3a W45L 1.00e+0 B.1.1.277
V6021 1083C>T synonymous_variant ORF1ab_pp1a P361P 1.00e+0 B.1.1.277
V6187 2244C>T synonymous_variant ORF1ab_pp1a P748P 1.00e+0 B.1.1.277
V9330 312G>T synonymous_variant M A104A 6.32e-1 B.1.1.277
V9610 234C>T synonymous_variant N S78S 1.00e+0 B.1.1.306
V3811 922G>T missense_variant S V308L 7.07e-1 B.1.1.316
V1810 8390C>T missense_variant ORF1ab_pp1a S2797F 8.16e-1 B.1.1.348
V963 3275C>T missense_variant ORF1ab_pp1a A1092V 8.16e-1 B.1.1.348
V4560 555G>T missense_variant ORF3a Q185H 8.26e-1 B.1.139
V5136 164C>T missense_variant ORF8 A55V 7.18e-1 B.1.139
V5781 *4360G>T downstream_gene_variant S None 8.67e-1 B.1.139
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 7.18e-1 B.1.139
V9736 871C>T synonymous_variant N L291L 7.10e-1 B.1.139
V474 1307C>T missense_variant ORF1ab_pp1a T436I 7.66e-1 B.1.1.416
V8811 1425C>T synonymous_variant S A475A 7.45e-1 B.1.1.416
V9829 78C>T synonymous_variant ORF10 Y26Y -6.71e-1 B.1.1.416
V1103 3859G>A missense_variant ORF1ab_pp1a V1287M 1.00e+0 B.1.1.432
V1999 9923C>T missense_variant ORF1ab_pp1a T3308I 1.00e+0 B.1.1.432
V2925 17227C>T missense_variant ORF1ab_pp1ab P5743S 1.00e+0 B.1.1.432
V9384 570C>T synonymous_variant M D190D 1.00e+0 B.1.1.432
V1385 5834C>T missense_variant ORF1ab_pp1a T1945I 7.07e-1 B.1.1.63
V7168 9765C>T synonymous_variant ORF1ab_pp1a T3255T 8.66e-1 B.1.1.63
V9543 270C>T synonymous_variant ORF8 C90C 8.66e-1 B.1.1.63
V3454 20873A>G missense_variant ORF1ab_pp1ab K6958R 8.16e-1 B.1.177.16
V5666 -15G>T upstream_gene_variant ORF10 None 9.17e-1 B.1.177.20
V1111 3901A>G missense_variant ORF1ab_pp1a I1301V 1.00e+0 B.1.177.32
V1641 7166C>T missense_variant ORF1ab_pp1a S2389L 1.00e+0 B.1.177.32
V7061 8955G>A synonymous_variant ORF1ab_pp1a R2985R 1.00e+0 B.1.177.32
V8497 20187C>T synonymous_variant ORF1ab_pp1ab N6729N 7.07e-1 B.1.177.32
V8601 21042C>T synonymous_variant ORF1ab_pp1ab R7014R 1.00e+0 B.1.177.32
V3580 203T>C missense_variant S I68T 1.00e+0 B.1.177.60
V7102 9294C>T synonymous_variant ORF1ab_pp1a Y3098Y 1.00e+0 B.1.177.6
V1992 9863C>T missense_variant ORF1ab_pp1a T3288I 8.22e-1 B.1.177.81
V6003 951T>C synonymous_variant ORF1ab_pp1a L317L 7.41e-1 B.1.177.81
V7360 11439C>T synonymous_variant ORF1ab_pp1a Y3813Y 7.01e-1 B.1.177.81
V8260 18222C>T synonymous_variant ORF1ab_pp1ab L6074L 7.09e-1 B.1.177.81
V4817 80G>T missense_variant ORF6 W27L 9.87e-1 B.1.177.83
V6422 4011C>T synonymous_variant ORF1ab_pp1a Y1337Y 1.00e+0 B.1.177.83
V8724 702C>T synonymous_variant S N234N 6.98e-1 B.1.177.83
V3018 17903C>T missense_variant ORF1ab_pp1ab P5968L 9.14e-1 B.1.177.86
V3475 20956G>T missense_variant ORF1ab_pp1ab A6986S 9.73e-1 B.1.177.86
V8172 17586C>T synonymous_variant ORF1ab_pp1ab G5862G 7.23e-1 B.1.177.87
V8862 1848C>T synonymous_variant S N616N 9.48e-1 B.1.177.87
V8923 2292C>T synonymous_variant S N764N 6.31e-1 B.1.177.87
V1231 4760C>T missense_variant ORF1ab_pp1a S1587L 1.00e+0 B.1.177.8
V6101 1695C>T synonymous_variant ORF1ab_pp1a A565A 6.31e-1 B.1.177.8
V9736 871C>T synonymous_variant N L291L 1.00e+0 B.1.177.8
V1112 3915G>T missense_variant ORF1ab_pp1a K1305N 6.11e-1 B.1.206
V5407 487C>A missense_variant N Q163K 7.07e-1 B.1.234
V592 1736G>A missense_variant ORF1ab_pp1a R579K 7.07e-1 B.1.240
V1319 5383A>C missense_variant ORF1ab_pp1a K1795Q 7.69e-1 B.1.241
V2765 15942G>T missense_variant ORF1ab_pp1ab E5314D 8.52e-1 B.1.241
V471 1293A>G missense_variant ORF1ab_pp1a I431M 9.80e-1 B.1.241
V5385 417G>T missense_variant N L139F 9.50e-1 B.1.241
V5582 1018G>A missense_variant N D340N 9.07e-1 B.1.241
V8265 18291C>T synonymous_variant ORF1ab_pp1ab D6097D 9.45e-1 B.1.241
V8407 19338C>T synonymous_variant ORF1ab_pp1ab N6446N 7.87e-1 B.1.241
V9582 105G>T synonymous_variant N A35A 8.20e-1 B.1.241
V3837 1099G>T missense_variant S V367F 1.00e+0 B.1.265
V4294 3788C>T missense_variant S P1263L 7.07e-1 B.1.265
V9235 684T>C synonymous_variant ORF3a V228V 1.00e+0 B.1.265
V1126 4020G>T missense_variant ORF1ab_pp1a E1340D 6.15e-1 B.1.351.2
V8096 17040C>T synonymous_variant ORF1ab_pp1ab V5680V 6.08e-1 B.1.351.2
V1315 5357C>T missense_variant ORF1ab_pp1a P1786L 1.00e+0 B.1.351.3
V1828 8507C>T missense_variant ORF1ab_pp1a T2836I 1.00e+0 B.1.351.3
V3962 1749G>T missense_variant S E583D 1.00e+0 B.1.351.3
V6318 3192C>T synonymous_variant ORF1ab_pp1a Y1064Y 8.29e-1 B.1.351
V8923 2292C>T synonymous_variant S N764N 7.07e-1 B.1.36.29
V309 617C>T missense_variant ORF1ab_pp1a A206V 1.00e+0 B.1.367
V4462 295G>T missense_variant ORF3a A99S 1.00e+0 B.1.367
V5456 602G>T missense_variant N S201I 1.00e+0 B.1.367
V9195 318C>T synonymous_variant ORF3a L106L 1.00e+0 B.1.367
V494 1348C>A missense_variant ORF1ab_pp1a L450I 7.07e-1 B.1.36.8
V7089 9186C>T synonymous_variant ORF1ab_pp1a Y3062Y 7.07e-1 B.1.36.8
V7318 11074C>T synonymous_variant ORF1ab_pp1a L3692L 7.07e-1 B.1.36.8
V8047 16690C>T synonymous_variant ORF1ab_pp1ab L5564L 7.07e-1 B.1.36.8
V8714 639G>T synonymous_variant S V213V 7.07e-1 B.1.36.8
V899 3039G>T missense_variant ORF1ab_pp1a E1013D 7.07e-1 B.1.36.8
V7358 11409C>T synonymous_variant ORF1ab_pp1a Y3803Y 6.66e-1 B.1.369
V8590 20991G>A synonymous_variant ORF1ab_pp1ab A6997A 8.16e-1 B.1.369
V5052 122G>T missense_variant ORF7b C41F 8.94e-1 B.1.371
V513 1442C>T missense_variant ORF1ab_pp1a S481F 7.06e-1 B.1.371
V5334 136C>T missense_variant N P46S 1.00e+0 B.1.396
V2927 17254C>T missense_variant ORF1ab_pp1ab L5752F 1.00e+0 B.1.409
V8112 17157C>T synonymous_variant ORF1ab_pp1ab H5719H 1.00e+0 B.1.409
V9755 945C>T synonymous_variant N F315F 1.00e+0 B.1.409
V2115 10818delG frameshift_variant ORF1ab_pp1a L3606fs 1.00e+0 B.1.416
V2857 16755G>T missense_variant ORF1ab_pp1ab E5585D 1.00e+0 B.1.416
V7061 8955G>A synonymous_variant ORF1ab_pp1a R2985R 1.00e+0 B.1.416
V2046 10345G>T missense_variant ORF1ab_pp1a V3449F 7.12e-1 B.1.427
V3525 26C>T missense_variant S P9L 7.08e-1 B.1.427
V4546 524C>T missense_variant ORF3a T175I 8.20e-1 B.1.427
V6371 3609C>T synonymous_variant ORF1ab_pp1a I1203I 9.13e-1 B.1.427
V6913 7827C>T synonymous_variant ORF1ab_pp1a L2609L 8.81e-1 B.1.427
V852 2875C>T missense_variant ORF1ab_pp1a P959S 7.65e-1 B.1.427
V9188 288C>T synonymous_variant ORF3a L96L 6.35e-1 B.1.427
V9783 1080C>T synonymous_variant N Y360Y 7.29e-1 B.1.427
V6324 3222C>T synonymous_variant ORF1ab_pp1a A1074A 7.07e-1 B.1.466.2
V9205 429C>T synonymous_variant ORF3a A143A 7.07e-1 B.1.466.2
V5402 466G>T missense_variant N A156S 8.45e-1 B.1.517
V5948 600C>T synonymous_variant ORF1ab_pp1a C200C 6.54e-1 B.1.517
V7128 9540G>T synonymous_variant ORF1ab_pp1a L3180L 8.45e-1 B.1.517
V7475 12204C>T synonymous_variant ORF1ab_pp1a A4068A 8.45e-1 B.1.517
V8307 18564C>T synonymous_variant ORF1ab_pp1ab V6188V 7.13e-1 B.1.517
V8521 20415G>T synonymous_variant ORF1ab_pp1ab P6805P 8.45e-1 B.1.517
V6445 4179G>T synonymous_variant ORF1ab_pp1a V1393V 9.12e-1 B.1.561
V6591 5247C>T synonymous_variant ORF1ab_pp1a N1749N 8.17e-1 B.1.561
V7482 12279A>G synonymous_variant ORF1ab_pp1a S4093S 7.06e-1 B.1.561
V7907 15618T>G synonymous_variant ORF1ab_pp1ab S5206S 9.42e-1 B.1.561
V891 3002C>T missense_variant ORF1ab_pp1a T1001I 6.27e-1 B.1.561
V7222 10191C>T synonymous_variant ORF1ab_pp1a F3397F 7.10e-1 B.1.575
V9391 621C>T synonymous_variant M N207N 6.77e-1 B.1.575
V184 245_253delGTCATGTTA disruptive_inframe_deletion ORF1ab_pp1a G82_M85delinsV 1.00e+0 B.1.582
V4994 346C>T missense_variant ORF7a L116F 1.00e+0 B.1.582
V8636 129C>T synonymous_variant S F43F 6.65e-1 B.1.587
V8907 2121C>T synonymous_variant S Y707Y 7.07e-1 B.1.595
V6457 4305C>T synonymous_variant ORF1ab_pp1a I1435I 1.00e+0 B.1.609
V1732 7866G>T missense_variant ORF1ab_pp1a K2622N 1.00e+0 B.1.617.1
V6981 8394A>G synonymous_variant ORF1ab_pp1a K2798K 7.07e-1 B.1.617.1
V4880 85G>T missense_variant ORF7a V29L 7.07e-1 B.1.623
V7148 9660A>T synonymous_variant ORF1ab_pp1a A3220A 7.07e-1 B.40
V9380 552G>A synonymous_variant M S184S 7.07e-1 B.40
V2587 14054C>T missense_variant ORF1ab_pp1ab T4685I 7.07e-1 BA.1.1.11
V7264 10524C>T synonymous_variant ORF1ab_pp1a D3508D 7.07e-1 BA.1.1.11
V3423 20666C>T missense_variant ORF1ab_pp1ab T6889M 7.07e-1 BA.1.1.16
V3711 556T>C missense_variant S F186L 7.07e-1 BA.1.1.16
V8359 18922C>T synonymous_variant ORF1ab_pp1ab L6308L 1.00e+0 BA.1.13.1
V3232 19384G>T missense_variant ORF1ab_pp1ab V6462L 7.07e-1 BA.1.14.1
V3814 968C>T missense_variant S T323I 6.69e-1 BA.1.14
V4413 179C>T missense_variant ORF3a S60F 8.16e-1 BA.1.15.2
V2151 10985G>T missense_variant ORF1ab_pp1a R3662L 7.07e-1 BA.1.1.7
V3737 641G>T missense_variant S R214L 7.07e-1 BA.1.1.7
V3822 1030G>T missense_variant S A344S 7.07e-1 BA.1.1.7
V3857 1231G>T missense_variant S A411S 7.07e-1 BA.1.1.7
V3923 1478A>T missense_variant S Q493L 7.07e-1 BA.1.1.7
V5056 127G>T missense_variant ORF7b A43S 7.07e-1 BA.1.1.7
V5061 -4G>T upstream_gene_variant ORF8 None 7.07e-1 BA.1.1.7
V5762 *4350G>T downstream_gene_variant S None 7.07e-1 BA.1.1.7
V5781 *4360G>T downstream_gene_variant S None 7.07e-1 BA.1.1.7
V5790 *4367G>T downstream_gene_variant S None 7.07e-1 BA.1.1.7
V8449 19719C>T synonymous_variant ORF1ab_pp1ab V6573V 7.07e-1 BA.1.1.7
V8592 20991G>T synonymous_variant ORF1ab_pp1ab A6997A 7.07e-1 BA.1.1.7
V8698 489G>T synonymous_variant S A163A 7.07e-1 BA.1.1.7
V8711 624G>T synonymous_variant S T208T 7.07e-1 BA.1.1.7
V8721 663G>T synonymous_variant S S221S 7.07e-1 BA.1.1.7
V7941 15828C>T synonymous_variant ORF1ab_pp1ab Y5276Y 1.00e+0 BA.1.19
V5491 637A>T missense_variant N N213Y 9.37e-1 BA.2.10.1
V6064 1419C>T synonymous_variant ORF1ab_pp1a I473I 1.00e+0 BA.2.11
V6561 5016C>T synonymous_variant ORF1ab_pp1a N1672N 1.00e+0 BA.2.11
V7876 15333T>C synonymous_variant ORF1ab_pp1ab Y5111Y 7.07e-1 BA.2.13
V713 2243C>T missense_variant ORF1ab_pp1a P748L 6.32e-1 BA.2.24
V6507 4662C>T synonymous_variant ORF1ab_pp1a D1554D 1.00e+0 BA.2.3.10
V7323 11109T>C synonymous_variant ORF1ab_pp1a D3703D 1.00e+0 BA.2.3.10
V407 1054G>A missense_variant ORF1ab_pp1a E352K 7.07e-1 BA.2.3.13
V178 245_250delGTCATG disruptive_inframe_deletion ORF1ab_pp1a G82_H83del 7.07e-1 BA.2.31
V4781 463C>T missense_variant M H155Y 7.07e-1 BA.2.3.20
V5962 678G>A synonymous_variant ORF1ab_pp1a R226R 1.00e+0 BA.2.3.20
V6493 4567C>T synonymous_variant ORF1ab_pp1a L1523L 1.00e+0 BA.2.3.20
V66 -63C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 BA.2.3.6
V4470 301C>T missense_variant ORF3a L101F 7.07e-1 BA.2.37
V3712 557T>C missense_variant S F186S 1.00e+0 BA.2.38.1
V454 1208C>T missense_variant ORF1ab_pp1a T403I 1.00e+0 BA.2.38.1
V7921 15688C>T synonymous_variant ORF1ab_pp1ab L5230L 1.00e+0 BA.2.38.1
V9623 330C>T synonymous_variant N F110F 6.31e-1 BA.2.38.1
V5339 187G>A missense_variant N D63N 7.06e-1 BA.2.38.2
V8964 2568C>T synonymous_variant S N856N 7.06e-1 BA.2.38.2
V5254 16C>A missense_variant N P6T 1.00e+0 BA.2.40.1
V2207 11249C>T missense_variant ORF1ab_pp1a T3750I 7.07e-1 BA.2.44
V378 926C>A missense_variant ORF1ab_pp1a P309Q 1.00e+0 BA.2.45
V6899 7749T>C synonymous_variant ORF1ab_pp1a S2583S 1.00e+0 BA.2.49
V6487 4515C>T synonymous_variant ORF1ab_pp1a I1505I 6.29e-1 BA.2.65
V1459 6184C>T missense_variant ORF1ab_pp1a L2062F 6.97e-1 BA.2.72
V7391 11637C>T synonymous_variant ORF1ab_pp1a L3879L 7.07e-1 BA.2.75.2
V8154 17469C>T synonymous_variant ORF1ab_pp1ab F5823F 7.07e-1 BA.2.7
V2428 13031A>G missense_variant ORF1ab_pp1a D4344G 1.00e+0 BA.2.9.3
V5342 199C>T missense_variant N P67S 7.07e-1 BA.2.9.3
V6507 4662C>T synonymous_variant ORF1ab_pp1a D1554D 7.07e-1 BA.4.1.8
V739 2327C>T missense_variant ORF1ab_pp1a A776V 7.07e-1 BA.4.1.8
V9566 45T>C synonymous_variant N I15I 7.07e-1 BA.4.1.8
V1347 5557C>T missense_variant ORF1ab_pp1a L1853F 9.64e-1 BA.4.6.4
V4273 3711G>T missense_variant S M1237I 8.16e-1 BA.4.6.5
V4967 280C>T stop_gained ORF7a Q94* 1.00e+0 BA.5.1.24
V5111 106C>T missense_variant ORF8 P36S 7.07e-1 BA.5.1.24
V8462 19851C>T synonymous_variant ORF1ab_pp1ab V6617V 7.07e-1 BA.5.1.24
V2180 11090C>T missense_variant ORF1ab_pp1a A3697V 1.00e+0 BA.5.1.28
V3771 751C>T missense_variant S P251S 8.98e-1 BA.5.1.30
V4977 293C>T missense_variant ORF7a S98F 8.54e-1 BA.5.1.30
V6583 5202C>T synonymous_variant ORF1ab_pp1a Y1734Y 7.16e-1 BA.5.1.30
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 8.83e-1 BA.5.1.5
V6778 6714T>G synonymous_variant ORF1ab_pp1a V2238V 8.52e-1 BA.5.1.5
V7034 8805T>C synonymous_variant ORF1ab_pp1a D2935D 8.52e-1 BA.5.1.5
V3228 19322C>T missense_variant ORF1ab_pp1ab T6441I 7.07e-1 BA.5.1.8
V8812 1431C>T synonymous_variant S S477S 7.07e-1 BA.5.1.9
V2744 15718G>A missense_variant ORF1ab_pp1ab V5240I 7.07e-1 BA.5.2.21
V8438 19632T>C synonymous_variant ORF1ab_pp1ab A6544A 7.07e-1 BA.5.2.21
V106 -14G>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 BA.5.2.22
V1385 5834C>T missense_variant ORF1ab_pp1a T1945I 1.00e+0 BA.5.2.22
V2911 17075C>T missense_variant ORF1ab_pp1ab A5692V 1.00e+0 BA.5.2.22
V550 1619C>T missense_variant ORF1ab_pp1a A540V 1.00e+0 BA.5.2.22
V5533 755C>T missense_variant N A252V 1.00e+0 BA.5.2.22
V7794 14658C>T synonymous_variant ORF1ab_pp1ab I4886I 1.00e+0 BA.5.2.22
V8470 19971C>T synonymous_variant ORF1ab_pp1ab P6657P 1.00e+0 BA.5.2.22
V8586 20958A>T synonymous_variant ORF1ab_pp1ab A6986A 1.00e+0 BA.5.2.22
V9169 180C>T synonymous_variant ORF3a S60S 7.07e-1 BA.5.2.22
V9404 84T>C synonymous_variant ORF6 N28N 7.07e-1 BA.5.2.22
V9634 387C>T synonymous_variant N G129G 1.00e+0 BA.5.2.22
V4459 289G>T missense_variant ORF3a V97F 1.00e+0 BA.5.2.24
V3004 17824G>T missense_variant ORF1ab_pp1ab G5942W 9.82e-1 BA.5.2.27
V2073 10525C>T missense_variant ORF1ab_pp1a H3509Y 8.16e-1 BA.5.2.28
V5962 678G>A synonymous_variant ORF1ab_pp1a R226R 8.16e-1 BA.5.2.28
V3585 212C>T missense_variant S S71F 1.00e+0 BA.5.2.31
V5598 1090C>T missense_variant N P364S 1.00e+0 BA.5.2.4
V7176 9813C>T synonymous_variant ORF1ab_pp1a F3271F 1.00e+0 BA.5.2.4
V8390 19212A>G synonymous_variant ORF1ab_pp1ab L6404L 9.04e-1 BA.5.2.8
V7414 11760C>T synonymous_variant ORF1ab_pp1a S3920S 7.07e-1 BA.5.3.3
V9021 3054C>T synonymous_variant S I1018I 7.07e-1 BA.5.3.3
V1451 6163C>T missense_variant ORF1ab_pp1a P2055S 1.00e+0 BA.5.3.5
V8127 17238C>T synonymous_variant ORF1ab_pp1ab F5746F 1.00e+0 BA.5.3.5
V2046 10345G>T missense_variant ORF1ab_pp1a V3449F 1.00e+0 BA.5.6.2
V2635 14567G>T missense_variant ORF1ab_pp1ab C4856F 8.16e-1 BA.5.6.2
V3655 441A>C missense_variant S K147N 8.33e-1 BE.10
V1642 7186A>G missense_variant ORF1ab_pp1a S2396G 6.32e-1 BE.1.1.1
V1826 8498A>G missense_variant ORF1ab_pp1a D2833G 7.74e-1 BE.1.1.1
V880 2974G>T missense_variant ORF1ab_pp1a D992Y 7.07e-1 BE.1.1.2
V8880 1968C>T synonymous_variant S V656V 7.07e-1 BE.1.1.2
V7203 10014C>T synonymous_variant ORF1ab_pp1a L3338L 8.81e-1 BE.1.2.1
V3733 638T>A missense_variant S V213E 7.07e-1 BE.4
V3778 757G>T missense_variant S D253Y 7.07e-1 BE.4
V7502 12504G>T synonymous_variant ORF1ab_pp1a A4168A 7.07e-1 BE.4
V1058 3638C>T missense_variant ORF1ab_pp1a P1213L 8.65e-1 BE.7
V5816 *4400C>T downstream_gene_variant S None 7.06e-1 BE.7
V7102 9294C>T synonymous_variant ORF1ab_pp1a Y3098Y 8.65e-1 BE.7
V7892 15474C>T synonymous_variant ORF1ab_pp1ab F5158F 8.65e-1 BE.7
V8927 2334C>T synonymous_variant S T778T 8.65e-1 BE.7
V921 3104C>T missense_variant ORF1ab_pp1a T1035I 9.12e-1 BF.11.1
V2587 14054C>T missense_variant ORF1ab_pp1ab T4685I 6.54e-1 BF.14
V9781 1074C>T synonymous_variant N D358D 7.07e-1 BF.21
V5391 430G>T missense_variant N D144Y 1.00e+0 BF.22
V2370 12485C>T missense_variant ORF1ab_pp1a A4162V 1.00e+0 BF.25
V456 1214C>T missense_variant ORF1ab_pp1a A405V 1.00e+0 BF.25
V6367 3552C>T synonymous_variant ORF1ab_pp1a D1184D 1.00e+0 BF.25
V7095 9243T>C synonymous_variant ORF1ab_pp1a N3081N 1.00e+0 BF.25
V4134 2816C>T missense_variant S S939F 6.67e-1 BF.26
V6302 3075G>T synonymous_variant ORF1ab_pp1a V1025V 7.07e-1 BF.28
V8552 20685T>C synonymous_variant ORF1ab_pp1ab D6895D 1.00e+0 BF.32
V2559 13919C>T missense_variant ORF1ab_pp1ab T4640I 6.54e-1 BF.4
V4647 803C>T missense_variant ORF3a T268M 8.89e-1 BF.4
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F 8.20e-1 BF.6
V3336 20056C>T missense_variant ORF1ab_pp1ab H6686Y 7.07e-1 BF.7.14
V3904 1442A>G missense_variant S N481S 1.00e+0 BF.7.14
V5282 55G>A missense_variant N G19R 1.00e+0 BF.7.14
V3413 20498C>T missense_variant ORF1ab_pp1ab T6833I 7.30e-1 BF.7.4.1
V6984 8418C>T synonymous_variant ORF1ab_pp1a I2806I 1.00e+0 BF.7.6
V7466 12141C>T synonymous_variant ORF1ab_pp1a N4047N 1.00e+0 BF.7.6
V7622 13356C>T synonymous_variant ORF1ab_pp1ab D4452D 8.66e-1 BF.7.6
V9511 51C>T synonymous_variant ORF8 H17H 1.00e+0 BF.7.6
V9762 972C>T synonymous_variant N V324V 8.16e-1 BF.7.6
V5838 27C>T synonymous_variant ORF1ab_pp1a N9N 1.00e+0 BK.1
V4342 85G>T missense_variant ORF3a V29F 6.66e-1 BL.1
V5800 *4376T>C downstream_gene_variant S None 7.45e-1 BL.1
V587 1714G>A missense_variant ORF1ab_pp1a G572R 6.66e-1 BL.1
V8036 16623C>T synonymous_variant ORF1ab_pp1ab Y5541Y 7.73e-1 BL.1
V8720 663G>A synonymous_variant S S221S 6.66e-1 BL.1
V221 328C>T missense_variant ORF1ab_pp1a H110Y 1.00e+0 BL.2
V3454 20873A>G missense_variant ORF1ab_pp1ab K6958R 1.00e+0 BL.2
V8036 16623C>T synonymous_variant ORF1ab_pp1ab Y5541Y 7.07e-1 BL.2
V4395 154C>T missense_variant ORF3a L52F 1.00e+0 BM.1.1.3
V4745 196G>T missense_variant M V66L 1.00e+0 BM.1.1.3
V7160 9720C>T synonymous_variant ORF1ab_pp1a D3240D 1.00e+0 BM.1.1.3
V7890 15462T>C synonymous_variant ORF1ab_pp1ab A5154A 7.07e-1 BM.1.1.3
V5490 635G>T missense_variant N G212V 1.00e+0 BM.4.1.1
V1023 3505G>A missense_variant ORF1ab_pp1a V1169I 1.00e+0 BN.1.2
V2647 14742G>T missense_variant ORF1ab_pp1ab E4914D 1.00e+0 BN.1.5
V5543 808G>T missense_variant N V270L 7.07e-1 BN.1.5
V5949 609C>T synonymous_variant ORF1ab_pp1a D203D 1.00e+0 BN.1.5
V8626 60C>T synonymous_variant S T20T 1.00e+0 BN.1.5
V3188 18945T>G missense_variant ORF1ab_pp1ab D6315E 8.16e-1 BN.1.9
V3189 18946A>G missense_variant ORF1ab_pp1ab R6316G 8.16e-1 BN.1.9
V3190 18950A>G missense_variant ORF1ab_pp1ab Y6317C 8.16e-1 BN.1.9
V3191 18953C>A missense_variant ORF1ab_pp1ab P6318H 8.16e-1 BN.1.9
V7096 9250C>T synonymous_variant ORF1ab_pp1a L3084L 8.66e-1 BN.1.9
V8361 18948A>G synonymous_variant ORF1ab_pp1ab R6316R 8.16e-1 BN.1.9
V2647 14742G>T missense_variant ORF1ab_pp1ab E4914D 8.16e-1 BN.1
V3305 19840C>T missense_variant ORF1ab_pp1ab L6614F 8.33e-1 BN.1
V5543 808G>T missense_variant N V270L 8.16e-1 BN.1
V5949 609C>T synonymous_variant ORF1ab_pp1a D203D 8.33e-1 BN.1
V1860 8633A>G missense_variant ORF1ab_pp1a N2878S 7.07e-1 BN.3.1
V7622 13356C>T synonymous_variant ORF1ab_pp1ab D4452D 7.07e-1 BN.3.1
V8546 20667G>A synonymous_variant ORF1ab_pp1ab T6889T 7.07e-1 BN.3.1
V3443 20776A>G missense_variant ORF1ab_pp1ab I6926V 7.07e-1 BQ.1.1.16
V3796 788C>T missense_variant S A263V 7.07e-1 BQ.1.1.16
V8354 18900C>T synonymous_variant ORF1ab_pp1ab D6300D 7.60e-1 BQ.1.12
V8973 2637G>T synonymous_variant S A879A 6.54e-1 BQ.1.12
V8112 17157C>T synonymous_variant ORF1ab_pp1ab H5719H 6.71e-1 BQ.1.1.31
V4502 383G>T missense_variant ORF3a W128L 1.00e+0 BQ.1.1.6
V6832 7152C>T synonymous_variant ORF1ab_pp1a Y2384Y 1.00e+0 BQ.1.1.6
V5086 49C>T missense_variant ORF8 H17Y 7.07e-1 BQ.1.1.8
V1315 5357C>T missense_variant ORF1ab_pp1a P1786L 7.07e-1 BQ.1.21
V1258 4910C>T missense_variant ORF1ab_pp1a T1637I 7.07e-1 BQ.1.22
V8884 1977A>T synonymous_variant S S659S 1.00e+0 BQ.1.22
V7049 8892T>C synonymous_variant ORF1ab_pp1a F2964F 7.75e-1 BQ.1.2
V8063 16803T>C synonymous_variant ORF1ab_pp1ab Y5601Y 7.75e-1 BQ.1.2
V2243 11495A>G missense_variant ORF1ab_pp1a K3832R 7.07e-1 BQ.1.3
V3392 20347C>T missense_variant ORF1ab_pp1ab L6783F 7.07e-1 BQ.1.3
V3495 21108G>T missense_variant ORF1ab_pp1ab Q7036H 7.07e-1 BQ.1.3
V4239 3565G>A missense_variant S V1189I 7.07e-1 BQ.1.3
V7049 8892T>C synonymous_variant ORF1ab_pp1a F2964F 7.07e-1 BQ.1.3
V8063 16803T>C synonymous_variant ORF1ab_pp1ab Y5601Y 7.07e-1 BQ.1.3
V7049 8892T>C synonymous_variant ORF1ab_pp1a F2964F 9.29e-1 BQ.1
V8063 16803T>C synonymous_variant ORF1ab_pp1ab Y5601Y 8.74e-1 BQ.1
V3211 19138C>T missense_variant ORF1ab_pp1ab H6380Y 1.00e+0 BY.1
V6014 1023C>T synonymous_variant ORF1ab_pp1a C341C 8.39e-1 BY.1
V6243 2607T>C synonymous_variant ORF1ab_pp1a N869N 6.73e-1 BY.1
V6701 6093G>A synonymous_variant ORF1ab_pp1a E2031E 8.58e-1 BY.1
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
V850 2857G>T missense_variant ORF1ab_pp1a D953Y 1.00e+0 C.36.3
V1099 3840G>T missense_variant ORF1ab_pp1a K1280N 7.07e-1 C.36
V3963 1753C>T missense_variant S L585F 7.07e-1 C.36
V5617 1132G>C missense_variant N E378Q 7.07e-1 C.36
V5734 *4321G>T downstream_gene_variant S None 7.07e-1 C.36
V3442 20770C>T missense_variant ORF1ab_pp1ab L6924F 7.65e-1 C.37
V5129 152C>T missense_variant ORF8 A51V 6.55e-1 C.37
V5197 305G>T missense_variant ORF8 C102F 7.80e-1 C.37
V5202 326dupT frameshift_variant ORF8 L109fs 7.18e-1 C.37
V5573 966G>T missense_variant N M322I 7.80e-1 C.37
V6215 2430C>T synonymous_variant ORF1ab_pp1a N810N 7.15e-1 C.37
V7195 9942C>T synonymous_variant ORF1ab_pp1a N3314N 7.18e-1 C.37
V8152 17457G>T synonymous_variant ORF1ab_pp1ab V5819V 6.66e-1 C.37
V8987 2787T>C synonymous_variant S S929S 8.40e-1 C.37
V5814 *4395G>T downstream_gene_variant S None 1.00e+0 CA.7
V9061 3348T>C synonymous_variant S T1116T 1.00e+0 CJ.1
V7676 13854G>A synonymous_variant ORF1ab_pp1ab T4618T 1.00e+0 CK.2.1.1
V211 292G>A missense_variant ORF1ab_pp1a G98S 1.00e+0 CP.1
V8487 20104C>T synonymous_variant ORF1ab_pp1ab L6702L 1.00e+0 CP.1
V3051 18062C>T missense_variant ORF1ab_pp1ab A6021V 1.00e+0 DF.1.1
V5396 451C>T missense_variant N P151S 7.07e-1 DL.1
V8250 18189T>C synonymous_variant ORF1ab_pp1ab A6063A 7.07e-1 DL.1
V1467 6211G>T missense_variant ORF1ab_pp1a V2071F 7.06e-1 N.5
V2142 10956G>T missense_variant ORF1ab_pp1a M3652I 7.06e-1 N.5
V3151 18742G>T missense_variant ORF1ab_pp1ab A6248S 7.06e-1 N.5
V3207 19124G>A missense_variant ORF1ab_pp1ab S6375N 7.06e-1 N.5
V8774 1128T>C synonymous_variant S T376T 7.06e-1 N.5
V4759 244A>G missense_variant M I82V 6.55e-1 P.1.15
V7186 9900C>T synonymous_variant ORF1ab_pp1a Y3300Y 1.00e+0 P.1.1
V9542 261A>G synonymous_variant ORF8 T87T 7.07e-1 P.1.1
V2329 12194C>T missense_variant ORF1ab_pp1a T4065I 8.16e-1 P.1.2
V6269 2787G>A synonymous_variant ORF1ab_pp1a E929E 7.07e-1 P.1.7
V2465 13295A>G missense_variant ORF1ab_pp1ab D4432G 6.14e-1 P.2
V8662 249C>T synonymous_variant S V83V 6.57e-1 P.2
V178 245_250delGTCATG disruptive_inframe_deletion ORF1ab_pp1a G82_H83del 7.07e-1 XAZ
V8858 1809T>C synonymous_variant S N603N 6.32e-1 XBB.1.9
V4745 196G>T missense_variant M V66L 6.33e-1 XBB.1
V108 -12C>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 XBB.2
V3789 776C>T missense_variant S T259I 7.07e-1 XBB.3
V6210 2397C>T synonymous_variant ORF1ab_pp1a Y799Y 1.00e+0 XBB.3
V2269 11755C>T missense_variant ORF1ab_pp1a L3919F 1.00e+0 XB
V6130 1872C>T synonymous_variant ORF1ab_pp1a L624L 1.00e+0 XB
V3305 19840C>T missense_variant ORF1ab_pp1ab L6614F 7.07e-1 XBK
V3608 284C>T missense_variant S T95I 7.07e-1 XBK
V616 1826C>T missense_variant ORF1ab_pp1a T609I 7.70e-1 AT.1
V9509 30C>T synonymous_variant ORF8 I10I 8.14e-1 AT.1
V531 1555G>A missense_variant ORF1ab_pp1a G519S 8.65e-1 AY.123.1
V6489 4530C>T synonymous_variant ORF1ab_pp1a S1510S 1.00e+0 AY.20.1
V1406 6020C>T missense_variant ORF1ab_pp1a T2007I 1.00e+0 AY.25.1.1
V4104 2540G>A missense_variant S R847K 1.00e+0 AY.25.1.1
V1013 3463G>T missense_variant ORF1ab_pp1a G1155C 1.00e+0 AY.3.2
V5937 558C>T synonymous_variant ORF1ab_pp1a V186V 1.00e+0 AY.3.2
V7914 15660C>T synonymous_variant ORF1ab_pp1ab Y5220Y 1.00e+0 AY.3.2
V3086 18274G>T missense_variant ORF1ab_pp1ab V6092L 8.14e-1 AY.43.7
V3561 98C>T missense_variant S T33I 7.67e-1 AY.43.7
V2378 12529G>A missense_variant ORF1ab_pp1a G4177R 8.15e-1 B.1.1.174
V7209 10104C>T synonymous_variant ORF1ab_pp1a R3368R 6.07e-1 B.1.1.174
V9252 795T>C synonymous_variant ORF3a D265D 8.15e-1 B.1.1.174
V2994 17759A>G missense_variant ORF1ab_pp1ab N5920S 1.00e+0 B.1.1.359
V3530 52C>T missense_variant S L18F 1.00e+0 B.1.1.359
V6425 4035G>T synonymous_variant ORF1ab_pp1a V1345V 1.00e+0 B.1.1.359
V7258 10482C>T synonymous_variant ORF1ab_pp1a N3494N 1.00e+0 B.1.1.359
V8770 1101C>T synonymous_variant S V367V 1.00e+0 B.1.1.359
V3119 18539G>T missense_variant ORF1ab_pp1ab S6180I 7.06e-1 B.1.1.397
V3783 767C>T missense_variant S S256L 7.06e-1 B.1.1.397
V4765 253G>T missense_variant M A85S 7.06e-1 B.1.1.397
V8790 1239G>T synonymous_variant S G413G 7.06e-1 B.1.1.397
V1113 3916G>T missense_variant ORF1ab_pp1a A1306S 1.00e+0 B.1.1.409
V2207 11249C>T missense_variant ORF1ab_pp1a T3750I 7.05e-1 B.1.1.409
V2873 16858G>T missense_variant ORF1ab_pp1ab A5620S 6.49e-1 B.1.146
V5153 194C>T missense_variant ORF8 A65V 1.00e+0 B.1.146
V5461 608G>A missense_variant N R203K -1.00e+0 B.1.1.500
V5465 610G>C missense_variant N G204R -1.00e+0 B.1.1.500
V9682 609G>A synonymous_variant N R203R -1.00e+0 B.1.1.500
V2711 15392C>T missense_variant ORF1ab_pp1ab T5131I 8.64e-1 B.1.1.521
V3781 761C>T missense_variant S S254F 1.00e+0 B.1.1.521
V4426 203G>T missense_variant ORF3a R68I 1.00e+0 B.1.1.521
V6026 1155C>T synonymous_variant ORF1ab_pp1a A385A 1.00e+0 B.1.1.521
V9133 3792G>T synonymous_variant S V1264V 1.00e+0 B.1.1.521
V1527 6416C>T missense_variant ORF1ab_pp1a A2139V 7.03e-1 B.1.1.57
V2304 11937G>T missense_variant ORF1ab_pp1a K3979N 7.03e-1 B.1.1.57
V4191 3310G>T missense_variant S V1104L 7.03e-1 B.1.1.57
V470 1286C>T missense_variant ORF1ab_pp1a A429V 7.03e-1 B.1.1.57
V5960 669C>T synonymous_variant ORF1ab_pp1a D223D 7.03e-1 B.1.1.57
V677 2041C>T missense_variant ORF1ab_pp1a L681F 7.03e-1 B.1.1.57
V7209 10104C>T synonymous_variant ORF1ab_pp1a R3368R 7.03e-1 B.1.1.57
V7878 15351C>T synonymous_variant ORF1ab_pp1ab H5117H 7.03e-1 B.1.1.57
V941 3203G>A missense_variant ORF1ab_pp1a G1068E 7.03e-1 B.1.1.57
V2444 13160G>A missense_variant ORF1ab_pp1a R4387H 1.00e+0 B.1.160.25
V1941 9338C>T missense_variant ORF1ab_pp1a T3113I 7.06e-1 B.1.177.33
V8303 18550C>T synonymous_variant ORF1ab_pp1ab L6184L 7.06e-1 B.1.177.33
V842 2831C>T missense_variant ORF1ab_pp1a S944L 7.06e-1 B.1.177.33
V9170 186C>T synonymous_variant ORF3a I62I 7.06e-1 B.1.177.33
V5596 1085C>T missense_variant N T362I 1.00e+0 B.1.195
V7951 15957G>T synonymous_variant ORF1ab_pp1ab P5319P 1.00e+0 B.1.195
V1426 6087G>T missense_variant ORF1ab_pp1a K2029N 1.00e+0 B.1.210
V1682 7586C>T missense_variant ORF1ab_pp1a A2529V 7.06e-1 B.1.210
V1696 7689G>T missense_variant ORF1ab_pp1a Q2563H 1.00e+0 B.1.210
V4015 2031G>T missense_variant S Q677H 7.06e-1 B.1.210
V5129 152C>T missense_variant ORF8 A51V 7.06e-1 B.1.210
V5601 1094C>T missense_variant N P365L 1.00e+0 B.1.210
V7401 11691C>T synonymous_variant ORF1ab_pp1a D3897D 1.00e+0 B.1.210
V7578 13032C>T synonymous_variant ORF1ab_pp1a D4344D 1.00e+0 B.1.210
V7966 16059C>T synonymous_variant ORF1ab_pp1ab C5353C 7.06e-1 B.1.210
V7930 15717C>T synonymous_variant ORF1ab_pp1ab I5239I 1.00e+0 B.1.223
V2697 15257T>A missense_variant ORF1ab_pp1ab F5086Y 6.96e-1 B.1.243.1
V5443 581C>T missense_variant N S194L -6.96e-1 B.1.243.1
V9623 330C>T synonymous_variant N F110F -1.00e+0 B.1.243.1
V2325 12145A>G missense_variant ORF1ab_pp1a I4049V 7.06e-1 B.1.332
V5087 52C>T stop_gained ORF8 Q18* 7.03e-1 B.1.333
V7427 11850C>T synonymous_variant ORF1ab_pp1a S3950S 1.00e+0 B.1.333
V1570 6671C>T missense_variant ORF1ab_pp1a S2224F 8.06e-1 B.1.36.34
V4846 -1C>T upstream_gene_variant ORF7a None 8.06e-1 B.1.36.34
V2434 13091C>T missense_variant ORF1ab_pp1a T4364I 1.00e+0 B.1.384
V4061 2240C>T missense_variant S T747I 7.06e-1 B.1.384
V147 133C>T missense_variant ORF1ab_pp1a H45Y 1.00e+0 B.1.433
V181 245_259delGTCATGTTATGGTTG disruptive_inframe_deletion ORF1ab_pp1a G82_V86del 1.00e+0 B.1.433
V3525 26C>T missense_variant S P9L 1.00e+0 B.1.433
V3638 432_434delTTA disruptive_inframe_deletion S Y145del 7.06e-1 B.1.433
V3739 643G>C missense_variant S D215H 1.00e+0 B.1.433
V3817 1015G>A missense_variant S G339S 1.00e+0 B.1.433
V3911 1451A>C missense_variant S E484A 1.00e+0 B.1.433
V3919 1468T>C missense_variant S F490L 1.00e+0 B.1.433
V4717 5C>T missense_variant M A2V 1.00e+0 B.1.433
V4835 163G>T stop_gained ORF6 E55* 1.00e+0 B.1.433
V5131 155G>T missense_variant ORF8 R52I 1.00e+0 B.1.433
V6221 2451C>T synonymous_variant ORF1ab_pp1a G817G 1.00e+0 B.1.433
V6333 3282T>C synonymous_variant ORF1ab_pp1a N1094N 1.00e+0 B.1.433
V8817 1482A>G synonymous_variant S S494S 1.00e+0 B.1.433
V8900 2049G>A synonymous_variant S R683R 1.00e+0 B.1.433
V1935 9261G>T missense_variant ORF1ab_pp1a M3087I 1.00e+0 B.1.459
V2639 14610G>T missense_variant ORF1ab_pp1ab K4870N 1.00e+0 B.1.459
V309 617C>T missense_variant ORF1ab_pp1a A206V 1.00e+0 B.1.459
V5810 *4389G>T downstream_gene_variant S None 1.00e+0 B.1.459
V6346 3354C>T synonymous_variant ORF1ab_pp1a V1118V 1.00e+0 B.1.459
V7195 9942C>T synonymous_variant ORF1ab_pp1a N3314N 7.06e-1 B.1.459
V9195 318C>T synonymous_variant ORF3a L106L 7.06e-1 B.1.459
V4535 512C>T missense_variant ORF3a S171L 7.05e-1 B.1.468
V4681 151C>T missense_variant E L51F 7.05e-1 B.1.468
V6739 6363C>T synonymous_variant ORF1ab_pp1a T2121T 7.05e-1 B.1.468
V6771 6631C>T synonymous_variant ORF1ab_pp1a L2211L 7.03e-1 B.1.468
V6828 7125C>T synonymous_variant ORF1ab_pp1a A2375A 7.05e-1 B.1.468
V1553 6548C>T missense_variant ORF1ab_pp1a T2183I 7.06e-1 B.1.474
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F 1.00e+0 B.1.558
V4476 310C>T missense_variant ORF3a P104S 1.00e+0 B.1.558
V5827 *4451C>T downstream_gene_variant S None 1.00e+0 B.1.558
V4438 232C>T missense_variant ORF3a H78Y 7.06e-1 B.1.627
V1483 6260C>T missense_variant ORF1ab_pp1a T2087I 9.33e-1 B.1.636
V4317 48G>T missense_variant ORF3a K16N 9.33e-1 B.1.636
V8062 16779T>C synonymous_variant ORF1ab_pp1ab Y5593Y 9.33e-1 B.1.636
V8293 18483C>T synonymous_variant ORF1ab_pp1ab V6161V 9.38e-1 B.1.636
V9348 385C>T synonymous_variant M L129L 9.33e-1 B.1.636
V9827 57C>T synonymous_variant ORF10 C19C 8.26e-1 B.1.636
V6869 7500C>T synonymous_variant ORF1ab_pp1a S2500S 1.00e+0 BA.1.1.5
V3997 1963C>T missense_variant S H655Y -7.06e-1 BA.2.34
V8194 17796C>T synonymous_variant ORF1ab_pp1ab L5932L 1.00e+0 BA.2.34
V9138 21C>T synonymous_variant ORF3a I7I 1.00e+0 BA.2.4
V3211 19138C>T missense_variant ORF1ab_pp1ab H6380Y 1.00e+0 BA.2.75.6
V6014 1023C>T synonymous_variant ORF1ab_pp1a C341C 1.00e+0 BA.2.75.6
V6701 6093G>A synonymous_variant ORF1ab_pp1a E2031E 7.05e-1 BA.2.75.6
V4647 803C>T missense_variant ORF3a T268M 1.00e+0 BA.2.75.7
V6014 1023C>T synonymous_variant ORF1ab_pp1a C341C 1.00e+0 BA.2.75.7
V6701 6093G>A synonymous_variant ORF1ab_pp1a E2031E 1.00e+0 BA.2.75.7
V7352 11385C>T synonymous_variant ORF1ab_pp1a G3795G 1.00e+0 BA.2.75.7
V3846 1150C>T missense_variant S P384S 1.00e+0 BA.4.1.3
V4085 2435C>T missense_variant S P812L 1.00e+0 BA.5.2.10
V8227 18048C>T synonymous_variant ORF1ab_pp1ab V6016V 1.00e+0 BA.5.2.10
V3733 638T>A missense_variant S V213E 9.12e-1 BE.4.2
V3735 638T>G missense_variant S V213G -6.08e-1 BE.4.2
V3778 757G>T missense_variant S D253Y 9.12e-1 BE.4.2
V7502 12504G>T synonymous_variant ORF1ab_pp1a A4168A 9.25e-1 BE.4.2
V1278 5045C>T missense_variant ORF1ab_pp1a T1682I 7.80e-1 BF.7.10
V4524 463G>T missense_variant ORF3a D155Y 9.03e-1 BF.7.10
V7023 8691C>T synonymous_variant ORF1ab_pp1a Y2897Y 9.38e-1 BF.7.10
V716 2258C>T missense_variant ORF1ab_pp1a T753I 9.03e-1 BF.7.10
V7448 12003G>A synonymous_variant ORF1ab_pp1a L4001L 9.43e-1 BF.7.10
V1568 6661C>T missense_variant ORF1ab_pp1a P2221S 1.00e+0 BF.7.9
V260 421_429delAAGTCATTT conservative_inframe_deletion ORF1ab_pp1a K141_F143del 7.06e-1 BF.7.9
V4604 686C>T missense_variant ORF3a T229I 7.06e-1 BF.7.9
V5057 128C>T missense_variant ORF7b A43V 1.00e+0 BF.7.9
V5305 90_98delAGAACGCAG disruptive_inframe_deletion N E31_S33del 1.00e+0 BF.7.9
V7609 13269A>G synonymous_variant ORF1ab_pp1ab V4423V 1.00e+0 BF.7.9
V7615 13302A>G synonymous_variant ORF1ab_pp1ab V4434V 1.00e+0 BF.7.9
V7814 14844C>T synonymous_variant ORF1ab_pp1ab T4948T 1.00e+0 BF.7.9
V9603 180C>T synonymous_variant N G60G 1.00e+0 BF.7.9
V3869 1331A>C missense_variant S K444T 7.05e-1 BJ.1
V3886 1355T>G missense_variant S L452R 7.05e-1 BJ.1
V3890 1380T>A missense_variant S N460K 1.00e+0 BJ.1
V4745 196G>T missense_variant M V66L 1.00e+0 BJ.1
V5383 408G>T missense_variant N E136D 7.05e-1 BJ.1
V8092 17004T>C synonymous_variant ORF1ab_pp1ab D5668D 1.00e+0 BM.1
V5180 251T>C missense_variant ORF8 L84S 7.06e-1 BM.2
V7969 16074C>T synonymous_variant ORF1ab_pp1ab V5358V 7.06e-1 BM.2
V9338 351C>T synonymous_variant M N117N 7.06e-1 BM.2
V3899 1432A>G missense_variant S T478A 7.06e-1 BN.1.3.3
V1891 8902T>C missense_variant ORF1ab_pp1a Y2968H 1.00e+0 BN.1.4.1
V3404 20476C>A missense_variant ORF1ab_pp1ab Q6826K 1.00e+0 BN.1.4.1
V6021 1083C>T synonymous_variant ORF1ab_pp1a P361P 1.00e+0 BN.1.4.1
V1187 4559C>T missense_variant ORF1ab_pp1a S1520F 1.00e+0 BN.1.8
V1593 6791C>T missense_variant ORF1ab_pp1a T2264I 1.00e+0 BN.1.8
V4459 289G>T missense_variant ORF3a V97F 1.00e+0 BQ.1.1.14
V6702 6096C>T synonymous_variant ORF1ab_pp1a D2032D 1.00e+0 BQ.1.1.14
V7049 8892T>C synonymous_variant ORF1ab_pp1a F2964F 1.00e+0 BQ.1.26
V8063 16803T>C synonymous_variant ORF1ab_pp1ab Y5601Y 1.00e+0 BQ.1.26
V190 251_259delTTATGGTTG disruptive_inframe_deletion ORF1ab_pp1a V84_V86del 1.00e+0 BS.1.1
V2436 13105G>A missense_variant ORF1ab_pp1a V4369I 1.00e+0 BS.1.1
V3723 626C>T missense_variant S P209L 1.00e+0 BS.1.1
V5737 *4322G>T downstream_gene_variant S None 1.00e+0 BS.1.1
V8126 17232A>G synonymous_variant ORF1ab_pp1ab E5744E 1.00e+0 BS.1.1
V8865 1854A>T synonymous_variant S T618T 1.00e+0 BS.1.1
V6662 5802T>C synonymous_variant ORF1ab_pp1a N1934N 7.06e-1 BT.1
V1171 4433C>T missense_variant ORF1ab_pp1a S1478F 7.06e-1 DQ.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 1.00e+0 N.3
V1555 6575C>T missense_variant ORF1ab_pp1a A2192V 1.00e+0 N.3
V5202 326dupT frameshift_variant ORF8 L109fs 1.00e+0 N.3
V4396 157C>T missense_variant ORF3a L53F 8.64e-1 P.6
V9537 222C>T synonymous_variant ORF8 I74I 1.00e+0 XBB.1.6
V2697 15257T>A missense_variant ORF1ab_pp1ab F5086Y 1.00e+0 XBC.1
V3454 20873A>G missense_variant ORF1ab_pp1ab K6958R 7.06e-1 XE





Manual curation of mutation (6725C>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