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The current mutation

ID: V6778
DNA: 6714T>G
Protein: V2238V
Position: 6979








COV2Var annotation categories







Summary information of mutation (6714T>G)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   6979
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   synonymous_variant
  DNA Level   DNA Mutation: 6714T>G
  Ref Seq: T
  Mut Seq: G
  Protein Level   Protein 1-letter Mutation: V2238V
  Protein 3-letter Mutation: Val2238Val

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 (6714T>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
2021-01 B.1.1.7 8 7 8.75e-1
2021-01 BF.5 8 1 1.25e-1
2021-10 BA.5.1.23 2 1 5.00e-1
2021-10 BF.10 2 1 5.00e-1
2021-11 AY.46.5 13 10 7.69e-1
2021-11 AY.122 13 3 2.31e-1
2021-12 AY.122 13 5 3.85e-1
2021-12 AY.46.5 13 4 3.08e-1
2021-12 AY.85 13 3 2.31e-1
2021-02 B.1.1.7 15 11 7.33e-1
2021-02 B.1.1.353 15 4 2.67e-1
2021-03 B.1.1.7 35 35 1.00e+0
2021-04 B.1.1.7 15 15 1.00e+0
2021-05 B.1.1.7 16 16 1.00e+0
2021-06 B.1.1.7 2 2 1.00e+0
2021-08 AY.98.1 1 1 1.00e+0
2021-09 AY.3 2 1 5.00e-1
2021-09 AY.44 2 1 5.00e-1
2022-01 BF.5 10 8 8.00e-1
2022-01 BA.1.1 10 2 2.00e-1
2022-10 BF.5 17271 10533 6.10e-1
2022-10 BF.10 17271 2523 1.46e-1
2022-10 BF.21 17271 697 4.04e-2
2022-11 BF.5 14248 10618 7.45e-1
2022-11 BF.10 14248 1214 8.52e-2
2022-11 BF.21 14248 434 3.05e-2
2022-12 BF.5 11695 9704 8.30e-1
2022-12 BF.10 11695 393 3.36e-2
2022-12 BF.5.1 11695 325 2.78e-2
2022-02 BF.5 5 3 6.00e-1
2022-02 BA.1.1 5 1 2.00e-1
2022-02 BN.1.5 5 1 2.00e-1
2022-03 BA.1.1 10 2 2.00e-1
2022-03 BA.2 10 2 2.00e-1
2022-03 BA.5 10 2 2.00e-1
2022-04 BF.1 105 69 6.57e-1
2022-04 BA.5 105 16 1.52e-1
2022-04 BF.28 105 9 8.57e-2
2022-05 BF.1 1394 665 4.77e-1
2022-05 BF.5 1394 219 1.57e-1
2022-05 BF.1.1 1394 107 7.68e-2
2022-06 BF.5 14104 4064 2.88e-1
2022-06 BF.1 14104 3784 2.68e-1
2022-06 BF.10 14104 1726 1.22e-1
2022-07 BF.5 37164 16095 4.33e-1
2022-07 BF.10 37164 5134 1.38e-1
2022-07 BF.1 37164 3848 1.04e-1
2022-08 BF.5 29977 14103 4.70e-1
2022-08 BF.10 29977 5422 1.81e-1
2022-08 BF.21 29977 2481 8.28e-2
2022-09 BF.5 22178 11797 5.32e-1
2022-09 BF.10 22178 4010 1.81e-1
2022-09 BF.21 22178 1552 7.00e-2
2023-01 BF.5 4853 4137 8.52e-1
2023-01 BF.5.1 4853 279 5.75e-2
2023-01 BF.10 4853 84 1.73e-2
2023-02 BF.5 405 326 8.05e-1
2023-02 BF.5.1 405 39 9.63e-2
2023-02 BF.25 405 11 2.72e-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
V6778 BF.10 9.78e-1 20574 2021-10-20 2023-2-8
V6778 BF.1 9.86e-1 10718 2022-4-11 2023-1-4
V6778 BF.21 9.84e-1 10044 2022-5-12 2023-1-30
V6778 BF.13 9.73e-1 2291 2022-6-9 2023-2-14
V6778 BF.15 9.62e-1 653 2022-6-16 2023-1-21
V6778 BF.16 9.80e-1 688 2022-5-29 2023-1-17
V6778 BF.18 1.91e-2 19 2022-5-17 2023-1-23
V6778 BF.22 9.98e-1 1566 2022-6-20 2023-2-14
V6778 BF.24 9.76e-1 736 2022-5-31 2023-2-5
V6778 BF.25 9.86e-1 1186 2022-4-25 2023-2-11
V6778 BF.2 9.84e-1 2311 2022-4-30 2023-2-14
V6778 BF.3 9.77e-1 1823 2022-5-3 2022-12-27
V6778 BF.5.1 9.98e-1 971 2022-6-26 2023-2-10
V6778 BF.9 9.91e-1 741 2022-5-28 2022-12-22
V6778 BF.27 9.58e-1 6489 2022-5-10 2023-1-25
V6778 BF.28 9.79e-1 8244 2022-3-30 2023-2-13
V6778 BF.5 9.90e-1 81614 2021-1-11 2023-2-17
V6778 B.1.1.353 4.00e-2 2 2020-9-8 2021-2-27
V6778 BF.10.1 9.96e-1 224 2022-6-29 2023-1-26
V6778 BF.1.1 9.85e-1 390 2022-4-28 2022-12-26
V6778 BF.20 9.64e-1 190 2022-5-24 2022-11-14
V6778 BF.23 9.10e-1 303 2022-5-6 2022-12-10
V6778 BF.29 9.91e-1 344 2022-6-28 2023-2-2
V6778 BF.3.1 9.78e-1 225 2022-5-25 2022-9-27
V6778 BF.34 9.84e-1 124 2022-8-19 2023-1-16
V6778 BF.5.2 1.00e+0 197 2022-9-4 2023-2-9
V6778 CM.8 1.06e-2 2 2022-9-6 2023-2-5
V6778 BA.5.2.1 3.57e-1 101494 2021-10-4 2023-2-20






Examining mutation (6714T>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 (6714T>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 2.41e-1 1.25e-1 1.92e+0 5.44e-2 Increase
Deceased -6.83e-2 2.55e-1 -2.67e-1 7.89e-1 Decrease
Homebound 3.47e-1 1.37e-1 2.53e+0 1.15e-2 Increase
Hospitalized 6.13e-3 8.23e-2 7.44e-2 9.41e-1 Increase
Mild -1.94e-1 1.97e-1 -9.85e-1 3.24e-1 Decrease
Recovered -4.80e-1 1.07e-1 -4.48e+0 7.48e-6 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 9.00e-2 2.06e-2 4.37e+0 1.26e-5 Increase
18-39 7.48e-2 9.94e-3 7.52e+0 5.36e-14 Increase
40-64 -3.26e-2 9.74e-3 -3.34e+0 8.33e-4 Decrease
65-84 -7.17e-2 1.22e-2 -5.87e+0 4.41e-9 Decrease
>=85 -7.26e-2 2.18e-2 -3.33e+0 8.69e-4 Decrease

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

Attribute Effect Estimate SE Z-value P-value Direction
Patient gender Male 3.34e-2 9.45e-3 3.54e+0 4.03e-4 Increase





Investigating natural selection at mutation (6714T>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

The FUBAR method within the HyPhy software was employed to analyze both positive and negative selection. FUBAR: pervasive selection on large datasets.
Note: List of sites found to be under pervasive selection by FUBAR (prob > 0.95). A prob[alpha < beta] value exceeding 0.95 indicates positive selection, while a prob[alpha > beta] value exceeding 0.95 indicates negative selection. "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site Prob[alpha>beta] Prob[alpha<beta] Lineage Method




Alterations in protein physicochemical properties induced by mutation (6714T>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




Alterations in protein stability induced by mutation (6714T>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




Impact on protein function induced by mutation (6714T>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




Exploring mutation (6714T>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 (6714T>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




Impact of spike protein mutation (6714T>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 (6714T>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 (6714T>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 (6714T>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
V9374 516A>G synonymous_variant M T172T 7.07e-1 B.1.1
V4398 160G>T missense_variant ORF3a A54S 6.12e-1 AY.85
V7558 12936G>A synonymous_variant ORF1ab_pp1a P4312P 1.00e+0 AY.85
V7846 15108G>T synonymous_variant ORF1ab_pp1ab T5036T 6.12e-1 AY.85
V2208 11251G>A missense_variant ORF1ab_pp1a V3751I 1.00e+0 BA.2.10.1
V619 1841C>T missense_variant ORF1ab_pp1a T614I 1.00e+0 BA.2.10.1
V6381 3729G>A synonymous_variant ORF1ab_pp1a L1243L 1.00e+0 BA.2.10.1
V9440 126C>T synonymous_variant ORF7a G42G 1.00e+0 BA.2.10.1
V2728 15584C>T missense_variant ORF1ab_pp1ab T5195I 8.25e-1 BA.2.12
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 6.84e-1 BA.2.12
V639 1912G>T missense_variant ORF1ab_pp1a G638C 9.03e-1 BA.2.12
V7155 9702C>T synonymous_variant ORF1ab_pp1a L3234L 9.35e-1 BA.2.12
V1529 6430C>T missense_variant ORF1ab_pp1a P2144S 1.00e+0 BA.2.75.5
V6102 1708C>T synonymous_variant ORF1ab_pp1a L570L 7.07e-1 BA.2.75.5
V6460 4314T>A synonymous_variant ORF1ab_pp1a L1438L 7.07e-1 BA.2.75.5
V6832 7152C>T synonymous_variant ORF1ab_pp1a Y2384Y 1.00e+0 BA.2.75.5
V6615 5389C>T synonymous_variant ORF1ab_pp1a L1797L 1.00e+0 BA.2.75
V6877 7569C>T synonymous_variant ORF1ab_pp1a N2523N 1.00e+0 BA.2.75
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 6.12e-1 BA.4.6.5
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 1.00e+0 BA.4.7
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 1.00e+0 BA.4.7
V1850 8617A>G missense_variant ORF1ab_pp1a I2873V 1.00e+0 BA.5.1.22
V1800 8351C>T missense_variant ORF1ab_pp1a A2784V 9.43e-1 BA.5.1.23
V778 2573C>T missense_variant ORF1ab_pp1a S858F 6.12e-1 BA.5.1.23
V281 496A>G missense_variant ORF1ab_pp1a S166G 7.90e-1 BA.5.1.24
V654 1975A>G missense_variant ORF1ab_pp1a I659V 8.94e-1 BA.5.1.24
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 8.94e-1 BA.5.1.30
V9374 516A>G synonymous_variant M T172T 7.07e-1 BA.5.1.3
V1574 6725C>T missense_variant ORF1ab_pp1a S2242F 8.52e-1 BA.5.1.5
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 6.46e-1 BA.5.1.5
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 9.42e-1 BA.5.1.5
V7034 8805T>C synonymous_variant ORF1ab_pp1a D2935D 9.09e-1 BA.5.1.5
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 7.07e-1 BA.5.1.6
V5397 452C>T missense_variant N P151L 6.14e-1 BA.5.2.20
V5273 37C>T missense_variant N P13S 1.00e+0 BA.5.2.23
V5871 213C>T synonymous_variant ORF1ab_pp1a I71I 1.00e+0 BA.5.2.23
V3223 19278G>T missense_variant ORF1ab_pp1ab M6426I 7.07e-1 BA.5.2.26
V6508 4665T>C synonymous_variant ORF1ab_pp1a N1555N 7.07e-1 BA.5.2.26
V6849 7329C>T synonymous_variant ORF1ab_pp1a G2443G 7.07e-1 BA.5.2.26
V9582 105G>T synonymous_variant N A35A 7.07e-1 BA.5.2.26
V4154 3058G>T missense_variant S A1020S 6.83e-1 BA.5.2.27
V4903 139C>T missense_variant ORF7a H47Y 6.70e-1 BA.5.2.27
V9374 516A>G synonymous_variant M T172T 6.79e-1 BA.5.2.27
V9591 129A>G synonymous_variant N Q43Q 6.52e-1 BA.5.2.27
V4154 3058G>T missense_variant S A1020S 8.16e-1 BA.5.2.28
V4903 139C>T missense_variant ORF7a H47Y 8.30e-1 BA.5.2.28
V7155 9702C>T synonymous_variant ORF1ab_pp1a L3234L 6.79e-1 BA.5.2.28
V8396 19260C>T synonymous_variant ORF1ab_pp1ab L6420L 7.87e-1 BA.5.2.28
V9225 621C>T synonymous_variant ORF3a F207F 7.85e-1 BA.5.2.28
V9591 129A>G synonymous_variant N Q43Q 7.86e-1 BA.5.2.28
V9631 378C>T synonymous_variant N N126N 6.37e-1 BA.5.2.28
V5667 -13C>A upstream_gene_variant ORF10 None 1.00e+0 BA.5.2.31
V3767 742T>C missense_variant S Y248H 1.00e+0 BA.5.2.34
V8298 18531C>T synonymous_variant ORF1ab_pp1ab N6177N 7.07e-1 BA.5.2.34
V1850 8617A>G missense_variant ORF1ab_pp1a I2873V 1.00e+0 BA.5.2.48
V3870 1331A>G missense_variant S K444R 1.00e+0 BA.5.2.4
V4154 3058G>T missense_variant S A1020S 7.07e-1 BA.5.2.4
V7007 8571C>T synonymous_variant ORF1ab_pp1a V2857V 1.00e+0 BA.5.2.4
V9178 234C>T synonymous_variant ORF3a H78H 1.00e+0 BA.5.2.4
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 8.00e-1 BA.5.2.9
V9446 156C>T synonymous_variant ORF7a N52N 6.66e-1 BA.5.3.1
V1850 8617A>G missense_variant ORF1ab_pp1a I2873V 1.00e+0 BA.5.3.3
V2318 12050G>A missense_variant ORF1ab_pp1a R4017K 7.07e-1 BA.5.3
V6251 2679G>A synonymous_variant ORF1ab_pp1a L893L 7.07e-1 BA.5.3
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 7.07e-1 BA.5.3
V9734 864C>T synonymous_variant N D288D 7.07e-1 BA.5.3
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 1.00e+0 BA.5.5.1
V3511 21256G>T missense_variant ORF1ab_pp1ab V7086F 1.00e+0 BE.1.1.1
V4222 3484C>T missense_variant S P1162S 1.00e+0 BE.1.1.1
V3614 291G>T missense_variant S K97N 1.00e+0 BE.3
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 1.00e+0 BE.3
V32 -126C>T upstream_gene_variant ORF1ab_pp1a None 6.32e-1 BE.5
V4154 3058G>T missense_variant S A1020S 1.00e+0 BE.5
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 7.99e-1 BE.5
V7155 9702C>T synonymous_variant ORF1ab_pp1a L3234L 1.00e+0 BE.5
V7802 14700A>G synonymous_variant ORF1ab_pp1ab K4900K 6.32e-1 BE.5
V8396 19260C>T synonymous_variant ORF1ab_pp1ab L6420L 6.18e-1 BE.5
V9374 516A>G synonymous_variant M T172T 1.00e+0 BE.5
V9569 57A>G synonymous_variant N G19G 8.44e-1 BE.5
V9591 129A>G synonymous_variant N Q43Q 1.00e+0 BE.5
V1392 5863C>T missense_variant ORF1ab_pp1a L1955F 1.00e+0 BE.7
V3616 293C>T missense_variant S S98F 7.06e-1 BE.7
V4569 584C>T missense_variant ORF3a S195F 1.00e+0 BE.7
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 7.06e-1 BE.7
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 1.00e+0 BE.7
V9564 39C>T synonymous_variant N P13P 7.06e-1 BE.7
V6538 4879C>T synonymous_variant ORF1ab_pp1a L1627L 7.71e-1 BF.11
V7593 13155A>G synonymous_variant ORF1ab_pp1a Q4385Q 9.13e-1 BF.11
V8850 1734T>C synonymous_variant S D578D 9.13e-1 BF.11
V548 1613C>T missense_variant ORF1ab_pp1a S538L 7.07e-1 BF.14
V9642 426A>T synonymous_variant N P142P 1.00e+0 BF.14
V4962 276A>C missense_variant ORF7a E92D 7.58e-1 BF.18
V6052 1329C>T synonymous_variant ORF1ab_pp1a S443S 7.58e-1 BF.18
V6102 1708C>T synonymous_variant ORF1ab_pp1a L570L 7.58e-1 BF.18
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 9.18e-1 BF.18
V6523 4755C>T synonymous_variant ORF1ab_pp1a D1585D 7.58e-1 BF.18
V7050 8895T>C synonymous_variant ORF1ab_pp1a P2965P 7.58e-1 BF.18
V7384 11568C>T synonymous_variant ORF1ab_pp1a A3856A 7.58e-1 BF.18
V8015 16411C>T synonymous_variant ORF1ab_pp1ab L5471L 7.58e-1 BF.18
V8603 21078C>T synonymous_variant ORF1ab_pp1ab Y7026Y 7.58e-1 BF.18
V9256 807G>T synonymous_variant ORF3a T269T 7.58e-1 BF.18
V1922 9175T>A missense_variant ORF1ab_pp1a C3059S 1.00e+0 BF.31
V4879 83C>T missense_variant ORF7a T28I 8.16e-1 BF.31
V5866 180T>C synonymous_variant ORF1ab_pp1a V60V 1.00e+0 BF.31
V9301 103C>T synonymous_variant M L35L 6.54e-1 BF.4
V1937 9269C>T missense_variant ORF1ab_pp1a T3090I 7.07e-1 BF.5.1
V9354 414C>T synonymous_variant M L138L -7.07e-1 BF.5.1
V281 496A>G missense_variant ORF1ab_pp1a S166G 6.66e-1 BF.6
V2900 17021C>T missense_variant ORF1ab_pp1ab S5674L 8.16e-1 BF.6
V2965 17486C>T missense_variant ORF1ab_pp1ab A5829V 8.16e-1 BF.6
V3249 19471G>T missense_variant ORF1ab_pp1ab D6491Y 1.00e+0 BF.7.1
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 1.00e+0 BF.7.1
V5311 94C>T missense_variant N R32C 1.00e+0 BM.1.1
V1390 5852C>T missense_variant ORF1ab_pp1a A1951V 1.00e+0 BN.1.2
V307 610C>T missense_variant ORF1ab_pp1a L204F 8.16e-1 BN.1.2
V7437 11895G>A synonymous_variant ORF1ab_pp1a E3965E 7.56e-1 BN.1.2
V7538 12754C>T synonymous_variant ORF1ab_pp1a L4252L 8.94e-1 BN.1.2
V1390 5852C>T missense_variant ORF1ab_pp1a A1951V 7.07e-1 BN.1.5
V307 610C>T missense_variant ORF1ab_pp1a L204F 1.00e+0 BN.1.5
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 7.07e-1 BN.1.5
V7538 12754C>T synonymous_variant ORF1ab_pp1a L4252L 7.07e-1 BN.1.5
V8887 1995C>T synonymous_variant S P665P 7.07e-1 BN.1.5
V7538 12754C>T synonymous_variant ORF1ab_pp1a L4252L 7.07e-1 BN.1
V8887 1995C>T synonymous_variant S P665P 7.07e-1 BN.1
V1608 6854C>T missense_variant ORF1ab_pp1a S2285F 1.00e+0 BQ.1.1.1
V3442 20770C>T missense_variant ORF1ab_pp1ab L6924F 7.07e-1 BQ.1.1.1
V373 914C>T missense_variant ORF1ab_pp1a P305L 1.00e+0 BQ.1.1.1
V4136 2821A>T missense_variant S T941S 6.66e-1 BQ.1.1.1
V5863 147C>T synonymous_variant ORF1ab_pp1a G49G 8.94e-1 BQ.1.1.1
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 6.03e-1 BQ.1.1.1
V6336 3297G>A synonymous_variant ORF1ab_pp1a V1099V 1.00e+0 BQ.1.1.1
V9801 1176G>T synonymous_variant N V392V 1.00e+0 BQ.1.11
V3601 248T>C missense_variant S V83A 1.00e+0 BQ.1.1.5
V3874 1333G>C missense_variant S V445L 1.00e+0 BQ.1.1.5
V3877 1336G>A missense_variant S G446S 7.07e-1 BQ.1.1.5
V3915 1456T>C missense_variant S F486L 1.00e+0 BQ.1.1.5
V8375 19062A>G synonymous_variant ORF1ab_pp1ab P6354P 7.07e-1 BQ.1.1.5
V4115 2612C>T missense_variant S A871V 7.07e-1 BQ.1
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 7.07e-1 BQ.1
V74 -56G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 BQ.1
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 8.16e-1 CL.1
V6799 6840C>T synonymous_variant ORF1ab_pp1a T2280T 7.07e-1 CM.2
V6489 4530C>T synonymous_variant ORF1ab_pp1a S1510S 1.00e+0 B.1.1.353
V4535 512C>T missense_variant ORF3a S171L 1.00e+0 BA.4.8
V4807 39G>T missense_variant ORF6 E13D 1.00e+0 BA.4.8
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 1.00e+0 BA.4.8
V7155 9702C>T synonymous_variant ORF1ab_pp1a L3234L 1.00e+0 BA.4.8
V1240 4787C>T missense_variant ORF1ab_pp1a P1596L 1.00e+0 BA.5.5.3
V2897 16995G>T missense_variant ORF1ab_pp1ab E5665D -1.00e+0 BF.10.1
V4596 668C>T missense_variant ORF3a T223I 7.06e-1 BF.10.1
V4663 26C>T missense_variant E T9I 1.00e+0 BF.10.1
V3735 638T>G missense_variant S V213G 6.11e-1 BF.1.1
V1907 9079C>T missense_variant ORF1ab_pp1a L3027F 7.04e-1 BF.34
V4742 187G>A missense_variant M A63T 7.04e-1 BF.34
V6842 7263C>T synonymous_variant ORF1ab_pp1a V2421V -7.04e-1 BF.34
V7082 9159A>G synonymous_variant ORF1ab_pp1a V3053V 7.04e-1 BF.34
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F -1.00e+0 BL.4
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 1.00e+0 BL.4
V7117 9468C>T synonymous_variant ORF1ab_pp1a F3156F 1.00e+0 BL.4
V8902 2073C>T synonymous_variant S S691S 1.00e+0 BL.4
V2124 10855A>G missense_variant ORF1ab_pp1a I3619V 1.00e+0 BS.1.1
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F -7.06e-1 BS.1.1
V2785 16154C>T missense_variant ORF1ab_pp1ab T5385I -7.06e-1 BS.1.1
V3987 1919C>T missense_variant S S640F -7.06e-1 BS.1.1
V5060 -5C>T upstream_gene_variant ORF8 None 1.00e+0 BS.1.1
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 1.00e+0 BS.1.1
V7437 11895G>A synonymous_variant ORF1ab_pp1a E3965E 1.00e+0 BS.1.1
V8284 18423C>T synonymous_variant ORF1ab_pp1ab C6141C 1.00e+0 BS.1.1
V8551 20682C>T synonymous_variant ORF1ab_pp1ab V6894V -7.06e-1 BS.1.1
V9569 57A>G synonymous_variant N G19G 1.00e+0 BS.1.1
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F -7.05e-1 BS.1
V2375 12524C>T missense_variant ORF1ab_pp1a T4175I 1.00e+0 BS.1
V3987 1919C>T missense_variant S S640F -7.05e-1 BS.1
V6316 3177T>C synonymous_variant ORF1ab_pp1a N1059N 1.00e+0 BS.1
V6370 3594A>G synonymous_variant ORF1ab_pp1a Q1198Q 1.00e+0 BS.1
V6866 7467C>T synonymous_variant ORF1ab_pp1a Y2489Y 1.00e+0 BS.1
V7437 11895G>A synonymous_variant ORF1ab_pp1a E3965E 7.05e-1 BS.1
V7881 15390C>T synonymous_variant ORF1ab_pp1ab D5130D -7.05e-1 BS.1
V7964 16044C>T synonymous_variant ORF1ab_pp1ab F5348F 1.00e+0 BS.1
V8551 20682C>T synonymous_variant ORF1ab_pp1ab V6894V -7.05e-1 BS.1
V2791 16210A>G missense_variant ORF1ab_pp1ab S5404G 1.00e+0 BY.1.1
V3091 18319G>A missense_variant ORF1ab_pp1ab V6107I 1.00e+0 BY.1.1
V3534 56C>T missense_variant S T19I -6.81e-1 BY.1.1
V3818 1015G>C missense_variant S G339R -6.81e-1 BY.1.1
V3820 1016G>A missense_variant S G339D -1.00e+0 BY.1.1
V3916 1456T>G missense_variant S F486V 1.00e+0 BY.1.1
V3940 1640C>T missense_variant S T547I 1.00e+0 BY.1.1
V4154 3058G>T missense_variant S A1020S 1.00e+0 BY.1.1
V5651 1237A>C missense_variant N S413R -6.81e-1 BY.1.1
V5871 213C>T synonymous_variant ORF1ab_pp1a I71I 1.00e+0 BY.1.1
V6557 4995T>A synonymous_variant ORF1ab_pp1a T1665T 1.00e+0 BY.1.1
V7193 9933C>T synonymous_variant ORF1ab_pp1a D3311D -6.81e-1 BY.1.1
V8180 17649C>T synonymous_variant ORF1ab_pp1ab N5883N 1.00e+0 BY.1.1
V9446 156C>T synonymous_variant ORF7a N52N 1.00e+0 BY.1.1
V9496 52C>T synonymous_variant ORF7b L18L -1.00e+0 BY.1.1
V9569 57A>G synonymous_variant N G19G 1.00e+0 BY.1.1
V3454 20873A>G missense_variant ORF1ab_pp1ab K6958R 7.06e-1 CA.1
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 1.00e+0 CA.1
V6446 4191C>T synonymous_variant ORF1ab_pp1a A1397A 1.00e+0 CA.1
V7251 10437C>T synonymous_variant ORF1ab_pp1a D3479D 1.00e+0 CA.1
V7437 11895G>A synonymous_variant ORF1ab_pp1a E3965E 7.06e-1 CA.1
V7550 12850C>T synonymous_variant ORF1ab_pp1a L4284L 1.00e+0 CA.1
V2697 15257T>A missense_variant ORF1ab_pp1ab F5086Y 1.00e+0 CM.8
V3989 1927T>C missense_variant S F643L 1.00e+0 CM.8
V9374 516A>G synonymous_variant M T172T 7.05e-1 CM.8





Manual curation of mutation (6714T>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