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The current mutation

ID: V2140
DNA: 10946A>G
Protein: Y3649C
Position: 11211








COV2Var annotation categories







Summary information of mutation (10946A>G)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   11211
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 10946A>G
  Ref Seq: A
  Mut Seq: G
  Protein Level   Protein 1-letter Mutation: Y3649C
  Protein 3-letter Mutation: Tyr3649Cys

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 (10946A>G) 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.1.36 32 13 4.06e-1
2020-10 B.1.36.7 32 10 3.12e-1
2020-10 B.1.1.33 32 4 1.25e-1
2020-11 B.1.36.7 63 52 8.25e-1
2020-11 B.1.36 63 5 7.94e-2
2020-11 B.1.160 63 4 6.35e-2
2020-12 B.1.36.7 84 61 7.26e-1
2020-12 B.1.438.1 84 6 7.14e-2
2020-12 B.1.177.12 84 3 3.57e-2
2020-04 B.28 1 1 1.00e+0
2020-05 B.1.1.33 3 2 6.67e-1
2020-05 B.1 3 1 3.33e-1
2020-06 B.1.1.33 6 6 1.00e+0
2020-07 B.1.1.33 5 4 8.00e-1
2020-07 B.1.36.7 5 1 2.00e-1
2020-08 B.1.1.33 13 7 5.38e-1
2020-08 B.1.1 13 3 2.31e-1
2020-08 B.1 13 1 7.69e-2
2020-09 B.1.36.7 12 8 6.67e-1
2020-09 B.1.1.33 12 2 1.67e-1
2020-09 B 12 1 8.33e-2
2021-01 B.1.36.7 185 95 5.14e-1
2021-01 B.1.438.1 185 82 4.43e-1
2021-01 B.1.177.12 185 3 1.62e-2
2021-10 B.1.160 1 1 1.00e+0
2021-12 AY.4 1 1 1.00e+0
2021-02 B.1.438.1 254 186 7.32e-1
2021-02 B.1.36.7 254 54 2.13e-1
2021-02 B.1.1.189 254 5 1.97e-2
2021-03 B.1.438.1 674 657 9.75e-1
2021-03 B.1.36.7 674 12 1.78e-2
2021-03 B.1.1.306 674 4 5.93e-3
2021-04 B.1.438.1 385 377 9.79e-1
2021-04 B.1.626 385 3 7.79e-3
2021-04 B.1 385 2 5.19e-3
2021-05 B.1.438.1 159 144 9.06e-1
2021-05 B.1.626 159 12 7.55e-2
2021-05 B.1.36.7 159 2 1.26e-2
2021-06 B.1.438.1 41 40 9.76e-1
2021-06 B.1.626 41 1 2.44e-2
2021-07 B.1.626 9 5 5.56e-1
2021-07 B.1.438.1 9 3 3.33e-1
2021-07 B.1.1.222 9 1 1.11e-1
2021-08 AY.27 1 1 1.00e+0
2021-09 B.1.160 1 1 1.00e+0

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
V2140 B.1.1.189 1.28e-2 8 2020-4-11 2021-10-16
V2140 B.1.36.7 9.74e-1 297 2020-7-7 2021-5-7
V2140 B.1.438.1 1.65e-1 1495 2020-9-16 2021-12-7
V2140 B.1.626 8.68e-2 21 2021-4-15 2021-10-14






Examining mutation (10946A>G) 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 (10946A>G) 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 -4.68e+1 1.90e+5 -2.47e-4 1.00e+0 Decrease
Deceased 3.39e+2 8.26e+4 4.11e-3 9.97e-1 Increase
Homebound -1.10e-14 1.08e+5 -1.02e-19 1.00e+0 Decrease
Hospitalized -2.06e+0 2.84e+0 -7.27e-1 4.67e-1 Decrease
Mild -9.15e-1 1.19e+0 -7.67e-1 4.43e-1 Decrease
Recovered -3.32e+1 1.58e+4 -2.10e-3 9.98e-1 Decrease

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

Attribute Effect Estimate SE Z-value P-value Direction
Patient age, years 0-17 7.36e-1 1.90e-1 3.88e+0 1.06e-4 Increase
18-39 -1.64e-1 1.21e-1 -1.35e+0 1.76e-1 Decrease
40-64 -7.29e-2 1.23e-1 -5.94e-1 5.52e-1 Decrease
65-84 -1.73e-1 1.85e-1 -9.35e-1 3.50e-1 Decrease
>=85 4.62e-1 3.21e-1 1.44e+0 1.50e-1 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 4.32e-2 1.18e-1 3.67e-1 7.13e-1 Increase





Investigating natural selection at mutation (10946A>G) site for genetic adaptation and diversity

Note: Investigating the occurrence of positive selection or negative selection at this mutation site reveals implications for genetic adaptation and diversity.

The MEME method within the HyPhy software was employed to analyze positive selection. MEME: episodic selection.
Note: List of sites found to be under episodic selection by MEME (p < 0.05). "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site P-value Lineage Method

The FEL method within the HyPhy software was employed to analyze both positive and negative selection. FEL: pervasive selection on samll datasets.
Note: List of sites found to be under pervasive selection by FEL (p < 0.05). A beta value greater than alpha signifies positive selection, while a beta value smaller than alpha signifies negative selection. "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site Alpha Beta P-value Lineage Method
nsp6 10973 11842 290 80 11.75 0.00 1.00e-2 B.1.525 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
nsp6 10973 11842 290 80 9.80e-1 1.00e-2 B.1.525 FUBAR




Alterations in protein physicochemical properties induced by mutation (10946A>G)

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 489928.88 6.04 542060 88.99 -0.022
Reference ORF1ab_pp1a 489988.91 6.04 543550 88.99 -0.023




Alterations in protein stability induced by mutation (10946A>G)

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
Y3649C ORF1ab_pp1a Point 3649 0.71 Increase 7 25 Environment
Y3649C ORF1ab_pp1a Point 3649 0.91 Increase 7.4 37 Internal




Impact on protein function induced by mutation (10946A>G)

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
Y3649C ORF1ab_pp1a Point 0.383 Altered Cytoplasmic_loop (Pr = 0.35 | P = 2.4e-05)
Altered PPI_hotspot (Pr = 0.30 | P = 4.4e-03)
Loss of Strand (Pr = 0.26 | P = 0.03)
Gain of Helix (Pr = 0.26 | P = 0.09)




Exploring mutation (10946A>G) 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 (10946A>G)

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
Y3649C ORF1ab_pp1a 11211 Chymotrypsin-high specificity NA
 TVAYFNMVYM (pos: 3649)
Y3649C ORF1ab_pp1a 11211 Proteinase K NA
 TVAYFNMVYM (pos: 3649)
Y3649C ORF1ab_pp1a 11211 Chymotrypsin-low specificity NA
 TVAYFNMVYM (pos: 3649)
Y3649C ORF1ab_pp1a 11211 Pepsin (pH>2) NA
 ATVAYFNMVY (pos: 3648)
Y3649C ORF1ab_pp1a 11211 NTCB (2-nitro-5-thiocyanobenzoic acid) ATVACFNMVY (pos: 3648)
 NA




Impact of spike protein mutation (10946A>G) 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 (10946A>G) 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.

        Show as:

        Show interface residues:





Impact of mutation (10946A>G) 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 (10946A>G) 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
V1606 6839C>T missense_variant ORF1ab_pp1a T2280I 1.00e+0 B.1.1.189
V3445 20794C>T missense_variant ORF1ab_pp1ab P6932S 8.65e-1 B.1.1.189
V4112 2576C>T missense_variant S T859I 8.93e-1 B.1.1.189
V553 1625G>A missense_variant ORF1ab_pp1a R542H 1.00e+0 B.1.1.189
V7784 14571T>C synonymous_variant ORF1ab_pp1ab D4857D 8.65e-1 B.1.1.189
V8772 1113C>T synonymous_variant S S371S 1.00e+0 B.1.1.189
V9045 3231T>C synonymous_variant S T1077T 1.00e+0 B.1.1.189
V2067 10496A>G missense_variant ORF1ab_pp1a K3499R 7.07e-1 B.1.1.222
V2789 16202C>T missense_variant ORF1ab_pp1ab P5401L 7.07e-1 B.1.1.222
V3525 26C>T missense_variant S P9L 7.07e-1 B.1.1.222
V3921 1469T>C missense_variant S F490S 7.07e-1 B.1.1.222
V5238 -1_1delAA frameshift_variant&start_lost N M1fs 7.07e-1 B.1.1.222
V553 1625G>A missense_variant ORF1ab_pp1a R542H 7.07e-1 B.1.1.222
V6974 8334T>C synonymous_variant ORF1ab_pp1a L2778L 7.07e-1 B.1.1.222
V7364 11472T>C synonymous_variant ORF1ab_pp1a N3824N 7.07e-1 B.1.1.222
V9045 3231T>C synonymous_variant S T1077T 7.07e-1 B.1.1.222
V1131 4055C>T missense_variant ORF1ab_pp1a A1352V 8.65e-1 B.1.1.306
V4619 760G>A missense_variant ORF3a G254R 9.43e-1 B.1.1.306
V4760 245T>C missense_variant M I82T 6.53e-1 B.1.1.306
V5081 32C>T missense_variant ORF8 T11I 9.04e-1 B.1.1.306
V5382 404C>T missense_variant N T135I 9.04e-1 B.1.1.306
V5614 1129G>T missense_variant N D377Y 6.10e-1 B.1.1.306
V5847 81C>T synonymous_variant ORF1ab_pp1a L27L 9.04e-1 B.1.1.306
V5915 414C>T synonymous_variant ORF1ab_pp1a A138A 8.31e-1 B.1.1.306
V5939 564C>T synonymous_variant ORF1ab_pp1a N188N 9.43e-1 B.1.1.306
V66 -63C>T upstream_gene_variant ORF1ab_pp1a None 6.53e-1 B.1.1.306
V783 2597C>T missense_variant ORF1ab_pp1a T866I 9.43e-1 B.1.1.306
V7477 12219C>T synonymous_variant ORF1ab_pp1a V4073V 9.52e-1 B.1.1.33
V8521 20415G>T synonymous_variant ORF1ab_pp1ab P6805P 9.67e-1 B.1.1.33
V4762 247G>A missense_variant M A83T 8.66e-1 B.1.160
V7354 11395T>C synonymous_variant ORF1ab_pp1a L3799L 8.66e-1 B.1.160
V5920 441C>T synonymous_variant ORF1ab_pp1a D147D 1.00e+0 B.1.177.12
V6676 5931C>T synonymous_variant ORF1ab_pp1a P1977P 1.00e+0 B.1.177.81
V7415 11766G>A synonymous_variant ORF1ab_pp1a Q3922Q 1.00e+0 B.1.177.81
V2841 16679G>T missense_variant ORF1ab_pp1ab S5560I 7.07e-1 B.1.234
V8669 285T>A synonymous_variant S T95T 1.00e+0 B.1.234
V6115 1791A>G synonymous_variant ORF1ab_pp1a V597V 1.00e+0 B.1.243
V8893 2028T>C synonymous_variant S T676T 1.00e+0 B.1.243
V7747 14346T>C synonymous_variant ORF1ab_pp1ab D4782D 7.23e-1 B.1.36
V3994 1958C>T missense_variant S A653V 9.86e-1 B.1.438.1
V4869 49C>T missense_variant ORF7a L17F 9.71e-1 B.1.438.1
V5255 17C>T missense_variant N P6L 9.98e-1 B.1.438.1
V9557 360C>T synonymous_variant ORF8 F120F 9.92e-1 B.1.438.1
V1935 9261G>T missense_variant ORF1ab_pp1a M3087I 1.00e+0 B.1.509
V2536 13729G>T missense_variant ORF1ab_pp1ab A4577S 1.00e+0 B.1.509
V2723 15502G>T missense_variant ORF1ab_pp1ab V5168L 1.00e+0 B.1.509
V2836 16625A>G missense_variant ORF1ab_pp1ab K5542R 1.00e+0 B.1.509
V4762 247G>A missense_variant M A83T 1.00e+0 B.1.509
V5512 702G>C missense_variant N M234I 1.00e+0 B.1.509
V5612 1126G>A missense_variant N A376T 1.00e+0 B.1.509
V6454 4278C>T synonymous_variant ORF1ab_pp1a T1426T 1.00e+0 B.1.509
V7336 11232C>T synonymous_variant ORF1ab_pp1a Y3744Y 1.00e+0 B.1.509
V7354 11395T>C synonymous_variant ORF1ab_pp1a L3799L 1.00e+0 B.1.509
V8315 18613C>T synonymous_variant ORF1ab_pp1ab L6205L 1.00e+0 B.1.509
V8805 1356G>T synonymous_variant S L452L 1.00e+0 B.1.509
V9314 213C>T synonymous_variant M Y71Y 1.00e+0 B.1.509
V9339 354T>C synonymous_variant M I118I 1.00e+0 B.1.509
V3037 17995A>G missense_variant ORF1ab_pp1ab I5999V 1.00e+0 B
V368 892G>T missense_variant ORF1ab_pp1a G298C 1.00e+0 B
V4357 109A>G missense_variant ORF3a I37V 1.00e+0 B
V7981 16149T>C synonymous_variant ORF1ab_pp1ab D5383D 1.00e+0 B
V1540 6469G>A missense_variant ORF1ab_pp1a V2157I 7.07e-1 C.16
V2896 16988G>T missense_variant ORF1ab_pp1ab R5663L 1.00e+0 C.16
V4143 2848G>A missense_variant S D950N 1.00e+0 C.16
V4560 555G>T missense_variant ORF3a Q185H 7.07e-1 C.16
V4622 766_768delGTT conservative_inframe_deletion ORF3a V256del 7.07e-1 C.16
V5240 -3A>G upstream_gene_variant N None 7.07e-1 C.16
V6656 5772C>T synonymous_variant ORF1ab_pp1a S1924S 7.07e-1 C.16
V3990 1937G>A missense_variant S R646H 1.00e+0 P.2
V7654 13701C>T synonymous_variant ORF1ab_pp1ab Y4567Y 1.00e+0 P.2
V1989 9851C>T missense_variant ORF1ab_pp1a T3284I 1.00e+0 B.1.626
V2091 10643C>T missense_variant ORF1ab_pp1a A3548V -9.51e-1 B.1.626
V2143 10957G>T missense_variant ORF1ab_pp1a V3653F -9.08e-1 B.1.626
V25 -160C>T upstream_gene_variant ORF1ab_pp1a None 7.41e-1 B.1.626
V393 998C>T missense_variant ORF1ab_pp1a T333M 1.00e+0 B.1.626
V6534 4839T>C synonymous_variant ORF1ab_pp1a H1613H 1.00e+0 B.1.626
V7045 8877C>T synonymous_variant ORF1ab_pp1a G2959G -9.51e-1 B.1.626
V8468 19914C>T synonymous_variant ORF1ab_pp1ab V6638V 9.47e-1 B.1.626
V4846 -1C>T upstream_gene_variant ORF7a None 1.00e+0 B.28





Manual curation of mutation (10946A>G)-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