Back to top

The current mutation

ID: V4158
DNA: 3080C>T
Protein: T1027I
Position: 24642








COV2Var annotation categories







Summary information of mutation (3080C>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp02
  Gene Name   S
  Gene Type   protein_coding
  Genome position   24642
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 3080C>T
  Ref Seq: C
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: T1027I
  Protein 3-letter Mutation: Thr1027Ile

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 (3080C>T) across geographic regions, temporal trends, and lineages

The count of genome sequences harboring this mutation and its distribution across global regions offer insights into regional variations.
Note: The distribution of mutation across 218 geographical regions. Color representation of genome sequence counts. The data is obtained from GISAID's metadata, specifically capturing the regional distribution of genomic sequences.



The dynamic count of genome sequences containing this mutation over time.
Note: Clicking the "Count" or "Cumulative Count" button toggles the view. Count represents the number of genome sequences per month. Cumulative count represents the accumulated total count up to the respective month. The data is obtained from GISAID's metadata, specifically capturing the collection date of genomic sequences.



For every time point represented in the graph above, identifying the top 3 lineages with the highest count of genome sequences carrying this mutation aids in pinpointing noteworthy lineages for further analysis.
Note: Users can filter the lineages by entering a "Year-Month" term in the search box. For example, entering 2020-01 will display lineages that appeared in January 2020. The data is obtained from GISAID's metadata, specifically capturing the collection date of genomic sequences.

Collection date Lineage Total lineage monthly counts Lineage-specific monthly counts Lineage-specific monthly frequency
2020-10 B.1.1.317 39 8 2.05e-1
2020-10 P.1 39 7 1.79e-1
2020-10 B.1.1 39 3 7.69e-2
2020-11 B.1.2 51 10 1.96e-1
2020-11 B.1.1 51 8 1.57e-1
2020-11 B.1.1.317 51 5 9.80e-2
2020-12 P.1 196 122 6.22e-1
2020-12 B.1.2 196 12 6.12e-2
2020-12 B.1 196 11 5.61e-2
2020-03 B.1.1 11 7 6.36e-1
2020-03 B.1.1.48 11 2 1.82e-1
2020-03 B.1 11 1 9.09e-2
2020-04 B.1.1 31 14 4.52e-1
2020-04 B.1 31 11 3.55e-1
2020-04 P.1 31 4 1.29e-1
2020-05 B.1.620 52 35 6.73e-1
2020-05 B.1.619 52 7 1.35e-1
2020-05 B.1 52 2 3.85e-2
2020-06 B.1 4 1 2.50e-1
2020-06 B.1.164 4 1 2.50e-1
2020-06 B.1.301 4 1 2.50e-1
2020-07 B.1 14 3 2.14e-1
2020-07 XB 14 3 2.14e-1
2020-07 B.1.1.284 14 2 1.43e-1
2020-08 B.1.369 16 5 3.12e-1
2020-08 B.52 16 2 1.25e-1
2020-08 P.1 16 2 1.25e-1
2020-09 B.1.499 22 6 2.73e-1
2020-09 B.1.1.317 22 3 1.36e-1
2020-09 B.1.1.253 22 2 9.09e-2
2021-01 P.1 824 559 6.78e-1
2021-01 B.1.2 824 28 3.40e-2
2021-01 P.1.1 824 24 2.91e-2
2021-10 B.1.617.2 1313 196 1.49e-1
2021-10 P.1 1313 144 1.10e-1
2021-10 P.1.15 1313 131 9.98e-2
2021-11 B.1.617.2 1266 441 3.48e-1
2021-11 AY.4 1266 148 1.17e-1
2021-11 AY.129 1266 80 6.32e-2
2021-12 B.1.617.2 768 238 3.10e-1
2021-12 AY.43 768 63 8.20e-2
2021-12 P.1 768 61 7.94e-2
2021-02 P.1 2841 1943 6.84e-1
2021-02 P.1.1 2841 337 1.19e-1
2021-02 P.1.14 2841 157 5.53e-2
2021-03 P.1 10890 6331 5.81e-1
2021-03 P.1.14 10890 2121 1.95e-1
2021-03 P.1.1 10890 406 3.73e-2
2021-04 P.1 26838 14415 5.37e-1
2021-04 P.1.14 26838 5950 2.22e-1
2021-04 P.1.17 26838 1294 4.82e-2
2021-05 P.1 27609 15058 5.45e-1
2021-05 P.1.14 27609 4800 1.74e-1
2021-05 P.1.17 27609 1324 4.80e-2
2021-06 P.1 25193 14025 5.57e-1
2021-06 P.1.14 25193 2609 1.04e-1
2021-06 P.1.17 25193 1796 7.13e-2
2021-07 P.1 20236 10802 5.34e-1
2021-07 P.1.14 20236 1427 7.05e-2
2021-07 P.1.7 20236 1229 6.07e-2
2021-08 P.1 9848 4554 4.62e-1
2021-08 P.1.7 9848 1463 1.49e-1
2021-08 P.1.15 9848 804 8.16e-2
2021-09 P.1 2836 733 2.58e-1
2021-09 P.1.7 2836 498 1.76e-1
2021-09 P.1.15 2836 313 1.10e-1
2022-01 BA.1.1 82 20 2.44e-1
2022-01 AY.43 82 14 1.71e-1
2022-01 BA.1 82 9 1.10e-1
2022-10 BA.5.2.22 13 4 3.08e-1
2022-10 BA.5.5 13 2 1.54e-1
2022-10 BA.5.3.3 13 1 7.69e-2
2022-11 BF.7 19 3 1.58e-1
2022-11 AY.127 19 2 1.05e-1
2022-11 BE.1.1.2 19 2 1.05e-1
2022-12 BF.7 23 5 2.17e-1
2022-12 BA.5.2.6 23 3 1.30e-1
2022-12 BF.5 23 2 8.70e-2
2022-02 BA.2 27 7 2.59e-1
2022-02 BA.1.1 27 6 2.22e-1
2022-02 BA.1.17.2 27 3 1.11e-1
2022-03 BA.2 46 34 7.39e-1
2022-03 BA.1.1 46 4 8.70e-2
2022-03 BA.2.9 46 2 4.35e-2
2022-04 BA.2 10 3 3.00e-1
2022-04 AY.119 10 2 2.00e-1
2022-04 B.1.177 10 1 1.00e-1
2022-05 P.1 19 5 2.63e-1
2022-05 BA.2 19 3 1.58e-1
2022-05 B.1.1.117 19 2 1.05e-1
2022-06 BA.2 21 3 1.43e-1
2022-06 BA.5.2.44 21 3 1.43e-1
2022-06 BA.1.1 21 2 9.52e-2
2022-07 BA.4.1 18 2 1.11e-1
2022-07 BA.5.5 18 2 1.11e-1
2022-07 P.1 18 2 1.11e-1
2022-08 BA.5.5 4 2 5.00e-1
2022-08 BA.5.9 4 1 2.50e-1
2022-08 BF.10 4 1 2.50e-1
2022-09 BA.5.6 20 11 5.50e-1
2022-09 BA.4.6 20 3 1.50e-1
2022-09 BF.5 20 2 1.00e-1
2023-01 BF.7 6 3 5.00e-1
2023-01 BA.5.2.49 6 1 1.67e-1
2023-01 BF.5 6 1 1.67e-1
2023-02 BQ.1.22 2 1 5.00e-1
2023-02 XBB.1.5 2 1 5.00e-1

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
V4158 AY.10 4.35e-2 63 2021-3-30 2021-12-8
V4158 AY.129 1.33e-2 206 2020-10-11 2022-2-25
V4158 B.1.1.349 2.75e-2 3 2020-8-4 2021-4-2
V4158 B.1.1.385 1.43e-2 4 2020-9-11 2021-10-12
V4158 B.1.1.523 9.73e-1 575 2021-2-2 2022-3-23
V4158 B.1.160.16 1.30e-2 14 2020-9-12 2021-8-9
V4158 B.1.301 1.23e-2 2 2020-4-1 2020-8-2
V4158 B.1.619 9.73e-1 1010 2020-3-10 2021-8-5
V4158 B.1.619.1 9.96e-1 1610 2021-2-22 2021-9-21
V4158 B.1.620 9.66e-1 1208 2020-4-5 2021-9-17
V4158 B.1.627 9.83e-1 467 2021-1-9 2021-8-21
V4158 B.1.631 9.83e-1 298 2020-12-16 2021-9-6
V4158 B.1.636 9.54e-1 103 2021-1-6 2021-7-10
V4158 B.52 2.17e-2 2 2020-3-12 2021-2-3
V4158 C.8 2.18e-2 5 2020-3-31 2021-1-4
V4158 P.1 9.85e-1 68836 2020-4-7 2022-7-23
V4158 P.1.1 9.81e-1 2617 2020-4-30 2021-10-17
V4158 P.1.10 9.75e-1 3406 2021-2-10 2021-10-29
V4158 P.1.10.1 1.00e+0 84 2021-4-25 2021-7-13
V4158 P.1.10.2 1.00e+0 24 2021-5-17 2021-7-8
V4158 P.1.11 1.00e+0 143 2021-5-10 2021-10-1
V4158 P.1.12 9.95e-1 1243 2020-12-23 2021-12-23
V4158 P.1.12.1 9.89e-1 174 2021-7-17 2021-12-6
V4158 P.1.13 9.65e-1 973 2021-2-24 2021-9-8
V4158 P.1.14 9.62e-1 17573 2020-11-3 2022-6-23
V4158 P.1.15 9.93e-1 4664 2021-1-6 2021-12-22
V4158 P.1.16 9.90e-1 2271 2021-1-31 2021-11-29
V4158 P.1.17 9.93e-1 6100 2021-2-23 2021-11-19
V4158 P.1.17.1 9.96e-1 1137 2021-4-2 2021-8-16
V4158 P.1.2 9.98e-1 1137 2021-1-28 2021-11-17
V4158 P.1.3 1.00e+0 29 2021-3-12 2021-6-30
V4158 P.1.4 1.00e+0 1077 2021-3-19 2021-11-11
V4158 P.1.5 1.00e+0 12 2021-4-3 2021-7-2
V4158 P.1.6 1.00e+0 574 2021-3-26 2021-11-16
V4158 P.1.7 9.97e-1 4298 2021-3-15 2021-12-1
V4158 P.1.7.1 9.93e-1 798 2021-2-7 2022-1-10
V4158 P.1.8 1.00e+0 295 2021-5-3 2021-10-25
V4158 P.1.9 1.00e+0 311 2021-4-9 2021-12-7
V4158 XB 9.82e-1 3137 2020-7-8 2021-9-29






Examining mutation (3080C>T) found in abundant sequences of non-human animal hosts

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

Animal host Lineage Source region Collection date Accession ID
Neovison vison B.1.22 Netherlands 2020-7-29 EPI_ISL_523087
Felis catus P.1 Brazil 2021-5-1 EPI_ISL_4565991
Felis catus B.1.619.1 South Korea 2021-6-30 EPI_ISL_15775583
Felis catus B.1.619.1 South Korea 2021-8-1 EPI_ISL_15727693
Odocoileus virginianus P.1 USA 2021-11-24 EPI_ISL_9347709
Odocoileus virginianus P.1 USA 2021-11-28 EPI_ISL_16297221
Odocoileus virginianus P.1 USA 2021-11-22 EPI_ISL_16318399
Odocoileus virginianus P.1 USA 2021-11-22 EPI_ISL_16297305
Odocoileus virginianus P.1 USA 2021-11-22 EPI_ISL_16318397
Odocoileus virginianus P.1 USA 2021-11-22 EPI_ISL_16297313
Odocoileus virginianus P.1 USA 2021-11-28 EPI_ISL_16308828
Odocoileus virginianus P.1 USA 2021-11-23 EPI_ISL_16297249
Odocoileus virginianus P.1 USA 2021-10-30 EPI_ISL_13610615
Odocoileus virginianus P.1 USA 2021-11-9 EPI_ISL_13610663
Odocoileus virginianus P.1 USA 2021-10-27 EPI_ISL_13610611
Odocoileus virginianus P.1 USA 2021-11-7 EPI_ISL_13610655
Odocoileus virginianus P.1 USA 2021-11-2 EPI_ISL_13610626
Odocoileus virginianus P.1 USA 2021-10-23 EPI_ISL_13610605
Odocoileus virginianus P.1 USA 2021-11-9 EPI_ISL_13610664
Odocoileus virginianus P.1 USA 2021-10-31 EPI_ISL_13610619
Odocoileus virginianus P.1 USA 2021-11-3 EPI_ISL_13658787
Odocoileus virginianus P.1 USA 2021-11-5 EPI_ISL_13610633
Odocoileus virginianus P.1 USA 2021-11-6 EPI_ISL_13610643
Odocoileus virginianus P.1 USA 2021-10-31 EPI_ISL_13610620
Odocoileus virginianus P.1 USA 2021-11-6 EPI_ISL_13610644
Odocoileus virginianus P.1 USA 2021-11-6 EPI_ISL_13610645
Odocoileus virginianus P.1 USA 2021-11-1 EPI_ISL_13610623
Odocoileus virginianus P.1 USA 2021-11-6 EPI_ISL_13610649
Odocoileus virginianus P.1 USA 2021-11-3 EPI_ISL_13610632
Odocoileus virginianus P.1 USA 2021-11-5 EPI_ISL_13610637
Odocoileus virginianus P.1 USA 2021-11-6 EPI_ISL_13658797
Odocoileus virginianus P.1 USA 2021-11-13 EPI_ISL_13610673
Odocoileus virginianus P.1 USA 2021-12-2 EPI_ISL_16297284
Canis lupus B.1.620 South Korea 2021-5-28 EPI_ISL_15775590
Canis lupus B.1.619.1 South Korea 2021-6-6 EPI_ISL_15775594
Canis lupus B.1.619.1 South Korea 2021-7-13 EPI_ISL_15727698
Canis lupus B.1.619.1 South Korea 2021-8-3 EPI_ISL_15727701




Association between mutation (3080C>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 -1.53e+0 2.45e-1 -6.22e+0 5.07e-10 Decrease
Deceased 1.14e+0 3.35e-1 3.42e+0 6.33e-4 Increase
Homebound -1.38e+0 2.00e+0 -6.88e-1 4.91e-1 Decrease
Hospitalized 1.47e-1 1.74e-1 8.45e-1 3.98e-1 Increase
Mild -2.00e+0 3.49e-1 -5.74e+0 9.20e-9 Decrease
Recovered 5.59e-1 2.15e-1 2.61e+0 9.18e-3 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 -3.32e-1 5.51e-2 -6.02e+0 1.75e-9 Decrease
18-39 1.98e-1 3.38e-2 5.85e+0 4.81e-9 Increase
40-64 2.13e-2 3.36e-2 6.33e-1 5.26e-1 Increase
65-84 -1.82e-1 4.76e-2 -3.82e+0 1.31e-4 Decrease
>=85 -7.27e-2 9.50e-2 -7.66e-1 4.44e-1 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 -2.35e-2 3.25e-2 -7.23e-1 4.70e-1 Decrease





Investigating natural selection at mutation (3080C>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
S 21563 25384 1273 1027 0.00e+0 BA.2.75 MEME
S 21563 25384 1273 1027 5.00e-2 XB MEME
S 21563 25384 1273 1027 4.00e-2 AY.69 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
S 21563 25384 1273 1027 14.35 0.00 2.00e-2 BQ.1.1.25 FEL
S 21563 25384 1273 1027 14.94 0.00 2.00e-2 BQ.1.18 FEL
S 21563 25384 1273 1027 0.00 15.99 3.00e-2 XB FEL
S 21563 25384 1273 1027 8.70 0.00 2.00e-2 BQ.1.1.32 FEL
S 21563 25384 1273 1027 0.00 8.87 4.00e-2 P.1 FEL
S 21563 25384 1273 1027 0.00 13.67 3.00e-2 AY.69 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
S 21563 25384 1273 1027 9.80e-1 1.00e-2 BQ.1.1.25 FUBAR
S 21563 25384 1273 1027 9.80e-1 1.00e-2 BQ.1.18 FUBAR
S 21563 25384 1273 1027 2.00e-2 9.60e-1 P.1.12 FUBAR
S 21563 25384 1273 1027 1.00e-2 9.60e-1 P.1.13 FUBAR
S 21563 25384 1273 1027 0.00e+0 9.90e-1 P.1.15 FUBAR
S 21563 25384 1273 1027 1.00e-2 9.80e-1 P.1.16 FUBAR
S 21563 25384 1273 1027 0.00e+0 9.80e-1 P.1.17 FUBAR
S 21563 25384 1273 1027 0.00e+0 9.80e-1 P.1.1 FUBAR
S 21563 25384 1273 1027 0.00e+0 9.90e-1 XB FUBAR
S 21563 25384 1273 1027 2.00e-2 9.60e-1 B.1.619 FUBAR
S 21563 25384 1273 1027 9.60e-1 3.00e-2 BQ.1.1.32 FUBAR
S 21563 25384 1273 1027 0.00e+0 9.90e-1 P.1 FUBAR
S 21563 25384 1273 1027 1.00e-2 9.70e-1 AY.69 FUBAR




Alterations in protein physicochemical properties induced by mutation (3080C>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 S 141190.53 6.24 146460 84.98 -0.075
Reference S 141178.47 6.24 146460 84.67 -0.079




Alterations in protein stability induced by mutation (3080C>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
T1027I S Point 1027 -0.22 Decrease 7 25 Environment
T1027I S Point 1027 -0.17 Decrease 7.4 37 Internal




Impact on protein function induced by mutation (3080C>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
T1027I S Point 0.091 Altered Coiled_coil (Pr = 0.29 | P = 0.01)
Altered MoRF (Pr = 0.25 | P = 0.07)
Gain of Zinc_binding at C1032 (Pr = 0.17 | P = 0.09)
Loss of Disulfide_linkage at C1032 (Pr = 0.11 | P = 0.05)
Altered Cytoplasmic_loop (Pr = 0.08 | P = 0.07)
Loss of Methylation at K1028 (Pr = 0.08 | P = 0.07)




Exploring mutation (3080C>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 (3080C>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
T1027I S 24642 Thermolysin NLAAIKMSEC (pos: 1026)
 NA




Impact of spike protein mutation (3080C>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
Mutation S S2 0.4046 -1.8668
Reference S S2 0.4057 -1.95857




Impact of mutation (3080C>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).

;
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 (3080C>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 (3080C>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
V3626 407G>T missense_variant S C136F 7.07e-1 BA.1.1.2
V9542 261A>G synonymous_variant ORF8 T87T 6.56e-1 AY.103
V7621 13353G>A synonymous_variant ORF1ab_pp1ab K4451K 6.32e-1 AY.125
V2210 11256G>A missense_variant ORF1ab_pp1a M3752I 6.44e-1 AY.39
V4645 799C>T missense_variant ORF3a P267S 6.53e-1 AY.39
V5339 187G>A missense_variant N D63N 6.05e-1 AY.39
V7852 15162A>G synonymous_variant ORF1ab_pp1ab V5054V 6.48e-1 AY.47
V8015 16411C>T synonymous_variant ORF1ab_pp1ab L5471L 7.39e-1 AY.47
V129 82G>A missense_variant ORF1ab_pp1a V28I 6.74e-1 B.1.617.2
V2132 10881G>T missense_variant ORF1ab_pp1a M3627I 8.04e-1 B.1.617.2
V3814 968C>T missense_variant S T323I 7.51e-1 B.1.617.2
V4154 3058G>T missense_variant S A1020S 7.12e-1 B.1.617.2
V4451 275C>T missense_variant ORF3a S92L 6.61e-1 B.1.617.2
V7348 11355C>T synonymous_variant ORF1ab_pp1a F3785F 6.66e-1 B.1.617.2
V7459 12063G>A synonymous_variant ORF1ab_pp1a K4021K 8.04e-1 B.1.617.2
V7677 13854G>T synonymous_variant ORF1ab_pp1ab T4618T 7.12e-1 B.1.617.2
V8451 19752C>T synonymous_variant ORF1ab_pp1ab D6584D 6.48e-1 B.1.617.2
V8915 2196C>T synonymous_variant S T732T 7.00e-1 B.1.617.2
V9341 363C>T synonymous_variant M N121N 6.81e-1 B.1.617.2
V9564 39C>T synonymous_variant N P13P 7.00e-1 B.1.617.2
V26 -156C>T upstream_gene_variant ORF1ab_pp1a None 6.73e-1 BA.5.6
V9574 84G>A synonymous_variant N Q28Q 7.45e-1 BA.5.6
V2210 11256G>A missense_variant ORF1ab_pp1a M3752I 8.89e-1 AY.102
V1953 9442A>G missense_variant ORF1ab_pp1a I3148V 8.16e-1 AY.107
V3555 79G>T missense_variant S A27S 8.16e-1 AY.107
V363 883G>T missense_variant ORF1ab_pp1a G295C 6.58e-1 AY.10
V129 82G>A missense_variant ORF1ab_pp1a V28I 8.46e-1 AY.110
V2132 10881G>T missense_variant ORF1ab_pp1a M3627I 9.20e-1 AY.110
V2494 13484A>G missense_variant ORF1ab_pp1ab K4495R 8.80e-1 AY.110
V2814 16462C>T missense_variant ORF1ab_pp1ab H5488Y 8.46e-1 AY.110
V3598 238G>T missense_variant S D80Y 9.20e-1 AY.110
V4154 3058G>T missense_variant S A1020S 8.15e-1 AY.110
V4451 275C>T missense_variant ORF3a S92L 7.89e-1 AY.110
V5684 10A>G missense_variant ORF10 I4V 8.80e-1 AY.110
V6187 2244C>T synonymous_variant ORF1ab_pp1a P748P 8.15e-1 AY.110
V7459 12063G>A synonymous_variant ORF1ab_pp1a K4021K 9.20e-1 AY.110
V7677 13854G>T synonymous_variant ORF1ab_pp1ab T4618T 9.20e-1 AY.110
V8451 19752C>T synonymous_variant ORF1ab_pp1ab D6584D 9.20e-1 AY.110
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 8.46e-1 AY.110
V8915 2196C>T synonymous_variant S T732T 8.80e-1 AY.110
V9341 363C>T synonymous_variant M N121N 7.39e-1 AY.110
V2132 10881G>T missense_variant ORF1ab_pp1a M3627I 7.00e-1 AY.112
V7459 12063G>A synonymous_variant ORF1ab_pp1a K4021K 7.45e-1 AY.112
V4429 214G>A missense_variant ORF3a A72T 1.00e+0 AY.113
V7079 9126C>T synonymous_variant ORF1ab_pp1a D3042D 7.07e-1 AY.113
V129 82G>A missense_variant ORF1ab_pp1a V28I 6.70e-1 AY.116.1
V2132 10881G>T missense_variant ORF1ab_pp1a M3627I 7.74e-1 AY.116.1
V2494 13484A>G missense_variant ORF1ab_pp1ab K4495R 7.74e-1 AY.116.1
V5129 152C>T missense_variant ORF8 A51V 7.74e-1 AY.116.1
V5684 10A>G missense_variant ORF10 I4V 7.74e-1 AY.116.1
V7459 12063G>A synonymous_variant ORF1ab_pp1a K4021K 7.74e-1 AY.116.1
V7677 13854G>T synonymous_variant ORF1ab_pp1ab T4618T 7.74e-1 AY.116.1
V8915 2196C>T synonymous_variant S T732T 7.74e-1 AY.116.1
V4450 268G>T missense_variant ORF3a V90F 7.07e-1 AY.116
V9629 348G>A synonymous_variant N G116G 8.16e-1 AY.116
V5964 687C>T synonymous_variant ORF1ab_pp1a Y229Y 1.00e+0 AY.120.1
V8025 16503C>T synonymous_variant ORF1ab_pp1ab N5501N 9.46e-1 AY.120
V4238 3564G>T missense_variant S E1188D 7.07e-1 AY.121.1
V5415 518C>T missense_variant N A173V 1.00e+0 AY.121.1
V1319 5383A>C missense_variant ORF1ab_pp1a K1795Q 6.32e-1 AY.127
V6131 1878C>A synonymous_variant ORF1ab_pp1a P626P 6.32e-1 AY.127
V7946 15906T>C synonymous_variant ORF1ab_pp1ab D5302D 6.32e-1 AY.127
V129 82G>A missense_variant ORF1ab_pp1a V28I 8.20e-1 AY.129
V2132 10881G>T missense_variant ORF1ab_pp1a M3627I 9.29e-1 AY.129
V3814 968C>T missense_variant S T323I 7.74e-1 AY.129
V4154 3058G>T missense_variant S A1020S 8.22e-1 AY.129
V4451 275C>T missense_variant ORF3a S92L 6.94e-1 AY.129
V6187 2244C>T synonymous_variant ORF1ab_pp1a P748P 8.19e-1 AY.129
V7348 11355C>T synonymous_variant ORF1ab_pp1a F3785F 7.99e-1 AY.129
V7459 12063G>A synonymous_variant ORF1ab_pp1a K4021K 8.66e-1 AY.129
V7677 13854G>T synonymous_variant ORF1ab_pp1ab T4618T 8.06e-1 AY.129
V8451 19752C>T synonymous_variant ORF1ab_pp1ab D6584D 8.32e-1 AY.129
V8915 2196C>T synonymous_variant S T732T 8.34e-1 AY.129
V9341 363C>T synonymous_variant M N121N 8.46e-1 AY.129
V9564 39C>T synonymous_variant N P13P 7.43e-1 AY.129
V4220 3457G>T missense_variant S D1153Y 8.94e-1 AY.131
V4398 160G>T missense_variant ORF3a A54S 8.94e-1 AY.131
V5180 251T>C missense_variant ORF8 L84S 8.94e-1 AY.131
V5508 687G>T missense_variant N Q229H 7.99e-1 AY.131
V7043 8865G>T synonymous_variant ORF1ab_pp1a V2955V 8.94e-1 AY.131
V8763 1035C>T synonymous_variant S T345T 6.31e-1 AY.131
V9483 339C>T synonymous_variant ORF7a C113C 7.74e-1 AY.131
V6768 6603T>C synonymous_variant ORF1ab_pp1a N2201N 7.07e-1 AY.16
V7515 12585A>G synonymous_variant ORF1ab_pp1a R4195R 7.07e-1 AY.16
V3751 725_733delTTGCTTTAC disruptive_inframe_deletion S L242_L244del 7.07e-1 AY.1
V3763 733C>T missense_variant S H245Y 1.00e+0 AY.1
V3252 19499C>T missense_variant ORF1ab_pp1ab T6500I 6.12e-1 AY.23
V9225 621C>T synonymous_variant ORF3a F207F 1.00e+0 AY.25.3
V3128 18616G>T missense_variant ORF1ab_pp1ab A6206S 7.07e-1 AY.28
V383 945G>T missense_variant ORF1ab_pp1a M315I 7.07e-1 AY.28
V5701 59G>T missense_variant ORF10 R20I 7.07e-1 AY.28
V6109 1761A>G synonymous_variant ORF1ab_pp1a T587T 7.07e-1 AY.28
V6120 1830G>A synonymous_variant ORF1ab_pp1a S610S 7.07e-1 AY.28
V2210 11256G>A missense_variant ORF1ab_pp1a M3752I 7.07e-1 AY.32
V4645 799C>T missense_variant ORF3a P267S 7.07e-1 AY.32
V5747 *4337C>T downstream_gene_variant S None 7.07e-1 AY.32
V5790 *4367G>T downstream_gene_variant S None 7.07e-1 AY.32
V6510 4671G>A synonymous_variant ORF1ab_pp1a K1557K 7.07e-1 AY.33
V5187 274G>A missense_variant ORF8 E92K 7.07e-1 AY.35
V2210 11256G>A missense_variant ORF1ab_pp1a M3752I 7.45e-1 AY.36.1
V5790 *4367G>T downstream_gene_variant S None 6.23e-1 AY.36.1
V8380 19122C>T synonymous_variant ORF1ab_pp1ab D6374D 7.45e-1 AY.36.1
V184 245_253delGTCATGTTA disruptive_inframe_deletion ORF1ab_pp1a G82_M85delinsV 9.07e-1 AY.39.1.3
V3630 422_433delTGGGTGTTTATT disruptive_inframe_deletion S L141_Y144del 1.00e+0 AY.39.1.4
V1817 8434A>G missense_variant ORF1ab_pp1a I2812V 7.07e-1 AY.39.1
V2210 11256G>A missense_variant ORF1ab_pp1a M3752I 7.07e-1 AY.39.1
V4645 799C>T missense_variant ORF3a P267S 7.07e-1 AY.39.1
V5339 187G>A missense_variant N D63N 7.07e-1 AY.39.1
V375 920C>T missense_variant ORF1ab_pp1a A307V 1.00e+0 AY.40
V4222 3484C>T missense_variant S P1162S 1.00e+0 AY.4.11
V7766 14460C>T synonymous_variant ORF1ab_pp1ab F4820F 7.07e-1 AY.4.11
V1308 5305A>G missense_variant ORF1ab_pp1a M1769V 1.00e+0 AY.41
V7894 15499C>T synonymous_variant ORF1ab_pp1ab L5167L 1.00e+0 AY.41
V1499 6308C>T missense_variant ORF1ab_pp1a S2103F 8.02e-1 AY.4.2.1
V2361 12469G>A missense_variant ORF1ab_pp1a G4157S 7.07e-1 AY.4.2.1
V1458 6181G>T missense_variant ORF1ab_pp1a V2061F 7.55e-1 AY.4.2.2
V9028 3141T>C synonymous_variant S Y1047Y 7.77e-1 AY.4.2.2
V6691 6054A>G synonymous_variant ORF1ab_pp1a P2018P 7.07e-1 AY.43.3
V7503 12513C>T synonymous_variant ORF1ab_pp1a Y4171Y 7.07e-1 AY.43.3
V7644 13596C>T synonymous_variant ORF1ab_pp1ab D4532D 7.07e-1 AY.43.3
V9557 360C>T synonymous_variant ORF8 F120F 7.07e-1 AY.43.3
V9648 447C>T synonymous_variant N R149R 7.07e-1 AY.43.3
V1195 4595A>G missense_variant ORF1ab_pp1a D1532G 7.07e-1 AY.43.8
V620 1852G>A missense_variant ORF1ab_pp1a G618S 7.07e-1 AY.43.8
V613 1816G>A missense_variant ORF1ab_pp1a V606I 7.07e-1 AY.4.5
V7845 15108G>A synonymous_variant ORF1ab_pp1ab T5036T 7.07e-1 AY.4.5
V4860 32C>T missense_variant ORF7a T11I 8.86e-1 AY.46.6
V7388 11601C>T synonymous_variant ORF1ab_pp1a C3867C 6.49e-1 AY.46.6
V7610 13272C>T synonymous_variant ORF1ab_pp1ab Y4424Y 7.07e-1 AY.4.9
V3593 227C>T missense_variant S T76I 7.07e-1 AY.53
V9621 318A>T synonymous_variant N P106P 1.00e+0 AY.59
V3555 79G>T missense_variant S A27S 7.07e-1 AY.62
V6292 2988C>T synonymous_variant ORF1ab_pp1a D996D 1.00e+0 AY.63
V181 245_259delGTCATGTTATGGTTG disruptive_inframe_deletion ORF1ab_pp1a G82_V86del 7.07e-1 AY.66
V361 881A>G missense_variant ORF1ab_pp1a D294G 7.07e-1 AY.66
V5067 10C>T missense_variant ORF8 L4F 7.07e-1 AY.66
V8451 19752C>T synonymous_variant ORF1ab_pp1ab D6584D 1.00e+0 AY.66
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S -7.32e-1 AY.69
V5456 602G>T missense_variant N S201I 6.54e-1 AY.69
V5462 608G>T missense_variant N R203M -6.04e-1 AY.69
V6619 5436T>C synonymous_variant ORF1ab_pp1a A1812A 6.68e-1 AY.69
V7840 15060C>T synonymous_variant ORF1ab_pp1ab N5020N 6.93e-1 AY.69
V8630 75C>T synonymous_variant S P25P 6.21e-1 AY.69
V9602 168C>T synonymous_variant N L56L 6.21e-1 AY.69
V1205 4634A>G missense_variant ORF1ab_pp1a H1545R 6.67e-1 AY.7.1
V4521 452C>T missense_variant ORF3a T151I 6.67e-1 AY.7.1
V7919 15678A>G synonymous_variant ORF1ab_pp1ab P5226P 8.04e-1 AY.7.1
V129 82G>A missense_variant ORF1ab_pp1a V28I 9.26e-1 AY.71
V2132 10881G>T missense_variant ORF1ab_pp1a M3627I 9.26e-1 AY.71
V2494 13484A>G missense_variant ORF1ab_pp1ab K4495R 9.13e-1 AY.71
V3598 238G>T missense_variant S D80Y 8.16e-1 AY.71
V3814 968C>T missense_variant S T323I 8.16e-1 AY.71
V4154 3058G>T missense_variant S A1020S 6.66e-1 AY.71
V4451 275C>T missense_variant ORF3a S92L 9.13e-1 AY.71
V5684 10A>G missense_variant ORF10 I4V 7.07e-1 AY.71
V7348 11355C>T synonymous_variant ORF1ab_pp1a F3785F 6.16e-1 AY.71
V7459 12063G>A synonymous_variant ORF1ab_pp1a K4021K 8.33e-1 AY.71
V7677 13854G>T synonymous_variant ORF1ab_pp1ab T4618T 9.26e-1 AY.71
V8451 19752C>T synonymous_variant ORF1ab_pp1ab D6584D 9.26e-1 AY.71
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 7.30e-1 AY.71
V8640 159C>T synonymous_variant S D53D 7.07e-1 AY.71
V8915 2196C>T synonymous_variant S T732T 8.33e-1 AY.71
V9341 363C>T synonymous_variant M N121N 7.21e-1 AY.71
V9564 39C>T synonymous_variant N P13P 7.30e-1 AY.71
V4851 13C>T missense_variant ORF7a L5F 1.00e+0 AY.7.2
V129 82G>A missense_variant ORF1ab_pp1a V28I 7.96e-1 AY.77
V2132 10881G>T missense_variant ORF1ab_pp1a M3627I 1.00e+0 AY.77
V2494 13484A>G missense_variant ORF1ab_pp1ab K4495R 8.81e-1 AY.77
V4154 3058G>T missense_variant S A1020S 1.00e+0 AY.77
V4451 275C>T missense_variant ORF3a S92L 9.25e-1 AY.77
V5557 887C>T missense_variant N T296I 1.00e+0 AY.77
V5684 10A>G missense_variant ORF10 I4V 7.96e-1 AY.77
V6187 2244C>T synonymous_variant ORF1ab_pp1a P748P 9.35e-1 AY.77
V7348 11355C>T synonymous_variant ORF1ab_pp1a F3785F 8.00e-1 AY.77
V7459 12063G>A synonymous_variant ORF1ab_pp1a K4021K 1.00e+0 AY.77
V7677 13854G>T synonymous_variant ORF1ab_pp1ab T4618T 9.35e-1 AY.77
V8451 19752C>T synonymous_variant ORF1ab_pp1ab D6584D 1.00e+0 AY.77
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 8.81e-1 AY.77
V8915 2196C>T synonymous_variant S T732T 1.00e+0 AY.77
V9341 363C>T synonymous_variant M N121N 8.81e-1 AY.77
V9564 39C>T synonymous_variant N P13P 1.00e+0 AY.77
V3726 629T>C missense_variant S I210T 7.07e-1 AY.78
V4129 2806G>A missense_variant S D936N 7.07e-1 AY.78
V6821 7038C>T synonymous_variant ORF1ab_pp1a I2346I 7.07e-1 AY.78
V7580 13077C>T synonymous_variant ORF1ab_pp1a D4359D 7.07e-1 AY.78
V7840 15060C>T synonymous_variant ORF1ab_pp1ab N5020N 7.07e-1 AY.78
V5804 *4380G>T downstream_gene_variant S None 1.00e+0 AY.84
V7610 13272C>T synonymous_variant ORF1ab_pp1ab Y4424Y 1.00e+0 AY.84
V3186 18916G>T missense_variant ORF1ab_pp1ab V6306L 7.07e-1 AY.85
V3535 59C>A missense_variant S T20N 7.07e-1 AY.85
V3606 283A>G missense_variant S T95A 7.07e-1 AY.85
V4310 35C>T missense_variant ORF3a T12I 7.07e-1 AY.85
V4436 229G>A missense_variant ORF3a V77I 7.07e-1 AY.85
V6126 1854C>T synonymous_variant ORF1ab_pp1a G618G 7.07e-1 AY.85
V9301 103C>T synonymous_variant M L35L 8.01e-1 AY.91
V1531 6434T>C missense_variant ORF1ab_pp1a F2145S 8.16e-1 AY.92
V3370 20213G>T missense_variant ORF1ab_pp1ab G6738V 8.16e-1 AY.92
V4483 322C>T missense_variant ORF3a L108F 6.66e-1 AY.92
V764 2456C>T missense_variant ORF1ab_pp1a A819V 8.16e-1 AY.92
V8202 17847T>C synonymous_variant ORF1ab_pp1ab P5949P 8.16e-1 AY.92
V8371 19026C>T synonymous_variant ORF1ab_pp1ab G6342G 8.16e-1 AY.92
V9252 795T>C synonymous_variant ORF3a D265D 8.66e-1 AY.93
V3722 629_631delTTA disruptive_inframe_deletion S I210del 6.67e-1 AY.98.1
V129 82G>A missense_variant ORF1ab_pp1a V28I 7.07e-1 AY.99.1
V2494 13484A>G missense_variant ORF1ab_pp1ab K4495R 7.07e-1 AY.99.1
V2814 16462C>T missense_variant ORF1ab_pp1ab H5488Y 7.07e-1 AY.99.1
V3534 56C>T missense_variant S T19I 7.07e-1 AY.99.1
V3598 238G>T missense_variant S D80Y 7.07e-1 AY.99.1
V4154 3058G>T missense_variant S A1020S 7.07e-1 AY.99.1
V5684 10A>G missense_variant ORF10 I4V 7.07e-1 AY.99.1
V7459 12063G>A synonymous_variant ORF1ab_pp1a K4021K 7.07e-1 AY.99.1
V7677 13854G>T synonymous_variant ORF1ab_pp1ab T4618T 7.07e-1 AY.99.1
V8451 19752C>T synonymous_variant ORF1ab_pp1ab D6584D 7.07e-1 AY.99.1
V8640 159C>T synonymous_variant S D53D 7.07e-1 AY.99.1
V8915 2196C>T synonymous_variant S T732T 7.07e-1 AY.99.1
V1348 5561C>T missense_variant ORF1ab_pp1a T1854I 1.00e+0 B.1.1.10
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F 1.00e+0 B.1.1.10
V3521 16G>T missense_variant S V6F 1.00e+0 B.1.1.10
V4263 3682G>T missense_variant S V1228L 7.07e-1 B.1.1.10
V4395 154C>T missense_variant ORF3a L52F 1.00e+0 B.1.1.10
V5243 -2A>T upstream_gene_variant N None 1.00e+0 B.1.1.10
V5490 635G>T missense_variant N G212V 1.00e+0 B.1.1.10
V6690 6045C>T synonymous_variant ORF1ab_pp1a S2015S 1.00e+0 B.1.1.10
V7185 9891C>T synonymous_variant ORF1ab_pp1a D3297D 1.00e+0 B.1.1.10
V7870 15282C>T synonymous_variant ORF1ab_pp1ab A5094A 1.00e+0 B.1.1.10
V804 2672C>T missense_variant ORF1ab_pp1a T891I 1.00e+0 B.1.1.10
V8964 2568C>T synonymous_variant S N856N 7.07e-1 B.1.1.10
V9259 819G>T synonymous_variant ORF3a V273V 1.00e+0 B.1.1.10
V8345 18852A>G synonymous_variant ORF1ab_pp1ab K6284K 7.07e-1 B.1.1.222
V3395 20365C>T missense_variant ORF1ab_pp1ab H6789Y 7.06e-1 B.1.126
V5602 1097C>T missense_variant N T366I 1.00e+0 B.1.126
V8367 18991C>T synonymous_variant ORF1ab_pp1ab L6331L 1.00e+0 B.1.126
V1507 6344G>T missense_variant ORF1ab_pp1a R2115I 1.00e+0 B.1.1.291
V2143 10957G>T missense_variant ORF1ab_pp1a V3653F 1.00e+0 B.1.1.291
V2434 13091C>T missense_variant ORF1ab_pp1a T4364I 7.07e-1 B.1.1.291
V2553 13862G>A missense_variant ORF1ab_pp1ab S4621N 1.00e+0 B.1.1.291
V2789 16202C>T missense_variant ORF1ab_pp1ab P5401L 1.00e+0 B.1.1.291
V3808 916T>C missense_variant S F306L 1.00e+0 B.1.1.291
V3924 1480T>C missense_variant S S494P 1.00e+0 B.1.1.291
V4535 512C>T missense_variant ORF3a S171L 1.00e+0 B.1.1.291
V4760 245T>C missense_variant M I82T 1.00e+0 B.1.1.291
V493 1345A>G missense_variant ORF1ab_pp1a N449D 1.00e+0 B.1.1.291
V5244 -1A>T upstream_gene_variant N None 1.00e+0 B.1.1.291
V5980 822A>G synonymous_variant ORF1ab_pp1a V274V 1.00e+0 B.1.1.291
V8040 16653G>A synonymous_variant ORF1ab_pp1ab L5551L 1.00e+0 B.1.1.291
V812 2704A>G missense_variant ORF1ab_pp1a M902V 1.00e+0 B.1.1.291
V9770 996C>T synonymous_variant N T332T 1.00e+0 B.1.1.291
V3783 767C>T missense_variant S S256L 7.74e-1 B.1.1.311
V1044 3606G>T missense_variant ORF1ab_pp1a K1202N 6.58e-1 B.1.1.317
V1265 4941G>T missense_variant ORF1ab_pp1a M1647I 9.04e-1 B.1.1.317
V1763 8069C>T missense_variant ORF1ab_pp1a A2690V 9.53e-1 B.1.1.317
V6602 5310C>T synonymous_variant ORF1ab_pp1a Y1770Y 7.37e-1 B.1.1.317
V759 2435C>T missense_variant ORF1ab_pp1a T812I 9.04e-1 B.1.1.317
V8744 870C>T synonymous_variant S D290D 8.51e-1 B.1.1.317
V9665 519A>T synonymous_variant N A173A 9.53e-1 B.1.1.317
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F 8.16e-1 B.1.1.33
V350 820G>T missense_variant ORF1ab_pp1a V274L 8.16e-1 B.1.1.33
V4499 378G>T missense_variant ORF3a R126S 8.16e-1 B.1.1.33
V5503 653C>T missense_variant N A218V 8.16e-1 B.1.1.33
V2897 16995G>T missense_variant ORF1ab_pp1ab E5665D 1.00e+0 B.1.1.348
V3860 1250A>C missense_variant S K417T 1.00e+0 B.1.1.348
V9804 1200G>A synonymous_variant N L400L 7.07e-1 B.1.1.348
V1609 6859C>T missense_variant ORF1ab_pp1a P2287S 6.66e-1 B.1.1.372
V3592 224G>T missense_variant S G75V 6.66e-1 B.1.1.372
V5924 468T>C synonymous_variant ORF1ab_pp1a D156D 8.16e-1 B.1.1.372
V6224 2484C>T synonymous_variant ORF1ab_pp1a D828D 8.16e-1 B.1.1.372
V5708 71G>T missense_variant ORF10 R24L 7.07e-1 B.1.1.420
V5884 262C>T synonymous_variant ORF1ab_pp1a L88L 1.00e+0 B.1.1.420
V1094 3806C>T missense_variant ORF1ab_pp1a T1269I 7.07e-1 B.1.1.50
V1984 9781G>A missense_variant ORF1ab_pp1a V3261I 1.00e+0 B.1.1.50
V241 364C>T missense_variant ORF1ab_pp1a L122F 7.07e-1 B.1.1.50
V28 -143C>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 B.1.1.50
V3052 18065C>T missense_variant ORF1ab_pp1ab T6022I 1.00e+0 B.1.1.50
V4366 119C>T missense_variant ORF3a S40L 1.00e+0 B.1.1.50
V4742 187G>A missense_variant M A63T 1.00e+0 B.1.1.50
V5237 1delA frameshift_variant&start_lost N M1fs 8.16e-1 B.1.1.50
V7764 14448G>T synonymous_variant ORF1ab_pp1ab V4816V 1.00e+0 B.1.1.50
V9002 2880C>T synonymous_variant S N960N 1.00e+0 B.1.1.50
V9060 3342C>T synonymous_variant S I1114I 1.00e+0 B.1.1.50
V8040 16653G>A synonymous_variant ORF1ab_pp1ab L5551L 6.79e-1 B.1.1.523
V4198 3350C>T missense_variant S T1117I 8.80e-1 B.1.160.16
V4543 520G>A missense_variant ORF3a G174S 9.25e-1 B.1.160.16
V7302 10887C>T synonymous_variant ORF1ab_pp1a V3629V 1.00e+0 B.1.160.16
V2137 10936A>G missense_variant ORF1ab_pp1a T3646A 1.00e+0 B.1.1.63
V2997 17768C>T missense_variant ORF1ab_pp1ab T5923I 7.07e-1 B.1.1.63
V4014 2031G>C missense_variant S Q677H 7.07e-1 B.1.1.63
V4627 767_769delTTA disruptive_inframe_deletion ORF3a V256_N257delinsD 7.07e-1 B.1.1.63
V4762 247G>A missense_variant M A83T 1.00e+0 B.1.1.63
V5237 1delA frameshift_variant&start_lost N M1fs 7.07e-1 B.1.1.63
V5747 *4337C>T downstream_gene_variant S None 1.00e+0 B.1.1.63
V9062 3351A>T synonymous_variant S T1117T 1.00e+0 B.1.1.63
V9645 435C>T synonymous_variant N H145H 7.07e-1 B.1.1.63
V30 -139G>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 B.1.1.70
V4817 80G>T missense_variant ORF6 W27L 7.07e-1 B.1.1.70
V4826 126G>T missense_variant ORF6 K42N 7.07e-1 B.1.1.70
V5110 103G>T missense_variant ORF8 D35Y 7.07e-1 B.1.1.70
V5870 210C>T synonymous_variant ORF1ab_pp1a F70F 7.07e-1 B.1.1.70
V9160 132A>G synonymous_variant ORF3a G44G 7.07e-1 B.1.1.70
V4057 2195C>T missense_variant S T732I 9.48e-1 B.1.177.10
V7228 10242C>T synonymous_variant ORF1ab_pp1a N3414N 8.31e-1 B.1.177.10
V8026 16527T>C synonymous_variant ORF1ab_pp1ab Y5509Y 9.48e-1 B.1.177.10
V4223 3485C>T missense_variant S P1162L 1.00e+0 B.1.177.15
V5539 794C>T missense_variant N T265I 6.65e-1 B.1.177.19
V1260 4913C>T missense_variant ORF1ab_pp1a T1638I 7.07e-1 B.1.177.42
V1430 6094G>A missense_variant ORF1ab_pp1a D2032N 1.00e+0 B.1.177.42
V2443 13159C>T missense_variant ORF1ab_pp1a R4387C 1.00e+0 B.1.177.42
V2575 13986G>T missense_variant ORF1ab_pp1ab L4662F 1.00e+0 B.1.177.42
V4449 268G>C missense_variant ORF3a V90L 1.00e+0 B.1.177.42
V7498 12489C>T synonymous_variant ORF1ab_pp1a C4163C 1.00e+0 B.1.177.42
V7758 14412C>T synonymous_variant ORF1ab_pp1ab P4804P 1.00e+0 B.1.177.42
V7840 15060C>T synonymous_variant ORF1ab_pp1ab N5020N 1.00e+0 B.1.177.42
V8266 18303T>C synonymous_variant ORF1ab_pp1ab N6101N 1.00e+0 B.1.177.42
V8747 888C>T synonymous_variant S L296L 1.00e+0 B.1.177.42
V8893 2028T>C synonymous_variant S T676T 1.00e+0 B.1.177.42
V9169 180C>T synonymous_variant ORF3a S60S 1.00e+0 B.1.177.42
V5024 41T>C missense_variant ORF7b L14S 7.07e-1 B.1.177.54
V9755 945C>T synonymous_variant N F315F 7.07e-1 B.1.177.54
V2666 14979G>T missense_variant ORF1ab_pp1ab M4993I 7.07e-1 B.1.177.81
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 7.73e-1 B.1.177.8
V6001 939C>T synonymous_variant ORF1ab_pp1a N313N 9.13e-1 B.1.177.8
V4449 268G>C missense_variant ORF3a V90L 1.00e+0 B.1.239
V4903 139C>T missense_variant ORF7a H47Y 1.00e+0 B.1.239
V5397 452C>T missense_variant N P151L 1.00e+0 B.1.239
V6676 5931C>T synonymous_variant ORF1ab_pp1a P1977P 1.00e+0 B.1.239
V2963 17483C>T missense_variant ORF1ab_pp1ab P5828L 6.07e-1 B.1.243
V5027 43G>T missense_variant ORF7b A15S 6.52e-1 B.1.243
V6796 6828C>T synonymous_variant ORF1ab_pp1a V2276V 9.05e-1 B.1.243
V5452 596C>T missense_variant N P199L 7.07e-1 B.1.258.17
V5985 837C>T synonymous_variant ORF1ab_pp1a S279S 8.16e-1 B.1.351.3
V1687 7604C>T missense_variant ORF1ab_pp1a S2535L 1.00e+0 B.1.356
V1942 9346C>T missense_variant ORF1ab_pp1a L3116F 1.00e+0 B.1.356
V1960 9491G>A missense_variant ORF1ab_pp1a R3164H 1.00e+0 B.1.356
V1974 9659C>T missense_variant ORF1ab_pp1a A3220V 1.00e+0 B.1.356
V3002 17822C>T missense_variant ORF1ab_pp1ab T5941I 1.00e+0 B.1.356
V3571 190T>A missense_variant S W64R 1.00e+0 B.1.356
V3665 458T>C missense_variant S M153T 1.00e+0 B.1.356
V4034 2063C>T missense_variant S A688V 1.00e+0 B.1.356
V4058 2203T>G missense_variant S S735A 1.00e+0 B.1.356
V4624 766_769delGTTA frameshift_variant ORF3a V256fs 1.00e+0 B.1.356
V4654 -23C>T upstream_gene_variant E None 1.00e+0 B.1.356
V6095 1647C>T synonymous_variant ORF1ab_pp1a S549S 1.00e+0 B.1.356
V6982 8397T>C synonymous_variant ORF1ab_pp1a H2799H 1.00e+0 B.1.356
V8463 19860T>A synonymous_variant ORF1ab_pp1ab I6620I 1.00e+0 B.1.356
V9002 2880C>T synonymous_variant S N960N 1.00e+0 B.1.356
V9396 12C>T synonymous_variant ORF6 L4L 1.00e+0 B.1.356
V9827 57C>T synonymous_variant ORF10 C19C 1.00e+0 B.1.356
V1263 4919C>T missense_variant ORF1ab_pp1a P1640L 1.00e+0 B.1.36.18
V3009 17851C>T missense_variant ORF1ab_pp1ab H5951Y 7.07e-1 B.1.36.18
V1428 6089C>T missense_variant ORF1ab_pp1a S2030L 1.00e+0 B.1.36.29
V5430 556T>C missense_variant N S186P 1.00e+0 B.1.369
V5636 1174G>T missense_variant N V392L 1.00e+0 B.1.369
V8011 16383G>T synonymous_variant ORF1ab_pp1ab T5461T 8.94e-1 B.1.369
V5958 660C>T synonymous_variant ORF1ab_pp1a D220D 6.12e-1 B.1.427
V7406 11718A>G synonymous_variant ORF1ab_pp1a E3906E 8.15e-1 B.1.499
V1459 6184C>T missense_variant ORF1ab_pp1a L2062F 7.07e-1 B.1.509
V1720 7819G>A missense_variant ORF1ab_pp1a E2607K 1.00e+0 B.1.509
V2090 10639A>G missense_variant ORF1ab_pp1a S3547G 1.00e+0 B.1.509
V2120 10844C>T missense_variant ORF1ab_pp1a A3615V 1.00e+0 B.1.509
V2845 16688C>T missense_variant ORF1ab_pp1ab T5563I 1.00e+0 B.1.509
V2879 16879C>T missense_variant ORF1ab_pp1ab R5627C 1.00e+0 B.1.509
V2993 17756G>A missense_variant ORF1ab_pp1ab R5919K 1.00e+0 B.1.509
V3525 26C>T missense_variant S P9L 1.00e+0 B.1.509
V3551 76C>T missense_variant S P26S 1.00e+0 B.1.509
V3861 1251G>T missense_variant S K417N 1.00e+0 B.1.509
V3894 1424C>T missense_variant S A475V 1.00e+0 B.1.509
V3919 1468T>C missense_variant S F490L 1.00e+0 B.1.509
V3997 1963C>T missense_variant S H655Y 7.07e-1 B.1.509
V5243 -2A>T upstream_gene_variant N None 1.00e+0 B.1.509
V5431 557C>T missense_variant N S186F 1.00e+0 B.1.509
V5978 798C>T synonymous_variant ORF1ab_pp1a F266F 1.00e+0 B.1.509
V6102 1708C>T synonymous_variant ORF1ab_pp1a L570L 1.00e+0 B.1.509
V6574 5100C>T synonymous_variant ORF1ab_pp1a Y1700Y 7.07e-1 B.1.509
V7257 10476C>T synonymous_variant ORF1ab_pp1a D3492D 7.07e-1 B.1.509
V9454 207C>T synonymous_variant ORF7a D69D 7.07e-1 B.1.509
V10 -200C>T upstream_gene_variant ORF1ab_pp1a None 6.74e-1 B.1.517
V1524 6407A>G missense_variant ORF1ab_pp1a D2136G 7.06e-1 B.1.517
V2844 16684C>T missense_variant ORF1ab_pp1ab P5562S 7.59e-1 B.1.517
V3574 192G>T missense_variant S W64C 8.01e-1 B.1.517
V5239 -3A>C upstream_gene_variant N None 6.04e-1 B.1.517
V6043 1263C>T synonymous_variant ORF1ab_pp1a A421A 8.01e-1 B.1.517
V7382 11559C>T synonymous_variant ORF1ab_pp1a I3853I 6.04e-1 B.1.517
V9438 120C>T synonymous_variant ORF7a Y40Y 7.55e-1 B.1.517
V9494 49C>T synonymous_variant ORF7b L17L 6.49e-1 B.1.517
V9557 360C>T synonymous_variant ORF8 F120F 7.12e-1 B.1.517
V5706 70C>T missense_variant ORF10 R24C 6.86e-1 B.1.526
V6913 7827C>T synonymous_variant ORF1ab_pp1a L2609L 6.69e-1 B.1.526
V7088 9183C>T synonymous_variant ORF1ab_pp1a A3061A 7.12e-1 B.1.526
V5602 1097C>T missense_variant N T366I 8.16e-1 B.1.565
V7220 10185C>T synonymous_variant ORF1ab_pp1a P3395P 1.00e+0 B.1.565
V3967 1839G>T missense_variant S Q613H 1.00e+0 B.1.577
V9304 159C>T synonymous_variant M F53F 6.32e-1 B.1.577
V9677 576C>T synonymous_variant N N192N 8.16e-1 B.1.577
V3250 19472A>G missense_variant ORF1ab_pp1ab D6491G 1.00e+0 B.1.609
V1080 3719C>T missense_variant ORF1ab_pp1a T1240I -6.11e-1 B.1.619.1
V3533 56C>G missense_variant S T19R -6.65e-1 B.1.619.1
V5462 608G>T missense_variant N R203M -6.11e-1 B.1.619.1
V1570 6671C>T missense_variant ORF1ab_pp1a S2224F 7.07e-1 B.1.621.1
V6246 2619T>C synonymous_variant ORF1ab_pp1a C873C 7.07e-1 B.1.621.1
V8884 1977A>T synonymous_variant S S659S 7.07e-1 B.1.621.1
V1287 5140A>G missense_variant ORF1ab_pp1a I1714V 7.07e-1 B.1.637
V6263 2757T>C synonymous_variant ORF1ab_pp1a H919H 7.07e-1 B.1.637
V292 545A>G missense_variant ORF1ab_pp1a Y182C 7.07e-1 BA.1.9
V6035 1206C>T synonymous_variant ORF1ab_pp1a R402R 7.06e-1 BA.1.9
V7281 10689C>T synonymous_variant ORF1ab_pp1a C3563C 8.16e-1 BA.1.9
V6732 6303C>T synonymous_variant ORF1ab_pp1a D2101D 7.07e-1 BA.2.12
V6288 2976C>T synonymous_variant ORF1ab_pp1a D992D 7.07e-1 BA.2.29
V3372 20219C>T missense_variant ORF1ab_pp1ab S6740F 7.07e-1 BA.2.3.17
V4716 4G>T missense_variant M A2S 7.07e-1 BA.2.3.17
V5548 835C>T missense_variant N P279S 1.00e+0 BA.2.48
V2969 17531C>T missense_variant ORF1ab_pp1ab A5844V 1.00e+0 BA.4.2
V6888 7671G>A synonymous_variant ORF1ab_pp1a A2557A 1.00e+0 BA.5.1.19
V8902 2073C>T synonymous_variant S S691S 1.00e+0 BA.5.1.19
V854 2887G>T missense_variant ORF1ab_pp1a G963C 7.07e-1 BA.5.2.20
V5144 184G>T missense_variant ORF8 V62L 8.94e-1 BA.5.2.22
V9148 99A>G synonymous_variant ORF3a A33A 7.07e-1 BA.5.2.33
V2911 17075C>T missense_variant ORF1ab_pp1ab A5692V 7.07e-1 BA.5.2.49
V7107 9333C>T synonymous_variant ORF1ab_pp1a Y3111Y 7.07e-1 BA.5.2.49
V8970 2631G>T synonymous_variant S L877L 1.00e+0 BA.5.3.3
V7282 10704C>T synonymous_variant ORF1ab_pp1a F3568F 8.16e-1 BE.1.1.2
V983 3343C>T missense_variant ORF1ab_pp1a L1115F 7.07e-1 BF.14
V5877 228T>C synonymous_variant ORF1ab_pp1a A76A 1.00e+0 BF.27
V3089 18295C>T missense_variant ORF1ab_pp1ab L6099F 1.00e+0 BF.7.14
V4166 3202G>A missense_variant S V1068I 1.00e+0 BF.7.14
V1720 7819G>A missense_variant ORF1ab_pp1a E2607K 7.07e-1 B
V3726 629T>C missense_variant S I210T 7.07e-1 B
V4129 2806G>A missense_variant S D936N 7.07e-1 B
V4872 66G>T missense_variant ORF7a E22D 7.07e-1 B
V6167 2142G>A synonymous_variant ORF1ab_pp1a K714K 7.07e-1 B
V6521 4743G>T synonymous_variant ORF1ab_pp1a T1581T 7.07e-1 B
V7842 15078C>T synonymous_variant ORF1ab_pp1ab A5026A 7.07e-1 BN.1.2
V5919 438C>T synonymous_variant ORF1ab_pp1a G146G 7.07e-1 BQ.1.1.23
V883 2978G>A missense_variant ORF1ab_pp1a G993D 7.07e-1 BQ.1.1.23
V6383 3744C>T synonymous_variant ORF1ab_pp1a F1248F 1.00e+0 C.36
V1198 4613C>T missense_variant ORF1ab_pp1a T1538I 1.00e+0 D.2
V1458 6181G>T missense_variant ORF1ab_pp1a V2061F 1.00e+0 DN.1
V2427 13010C>T missense_variant ORF1ab_pp1a P4337L 1.00e+0 DN.1
V8332 18747C>T synonymous_variant ORF1ab_pp1ab D6249D 1.00e+0 DN.1
V9823 30G>A synonymous_variant ORF10 P10P 1.00e+0 DN.1
V6691 6054A>G synonymous_variant ORF1ab_pp1a P2018P 6.31e-1 P.1.17.1
V7503 12513C>T synonymous_variant ORF1ab_pp1a Y4171Y 6.60e-1 P.1.1
V5241 -3A>T upstream_gene_variant N None -7.06e-1 P.1.7.1
V5274 38C>T missense_variant N P13L -7.06e-1 P.1.7.1
V4337 77C>T missense_variant ORF3a S26L 7.07e-1 XBB.1.1
V8021 16464T>C synonymous_variant ORF1ab_pp1ab H5488H 7.07e-1 XBB.1.1
V81 -47G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 XBB.1.1
V3608 284C>T missense_variant S T95I 1.00e+0 A.2.5.1
V3677 474A>C missense_variant S R158S 1.00e+0 A.2.5.1
V4022 2042C>A missense_variant S P681H 7.06e-1 A.2.5.1
V4034 2063C>T missense_variant S A688V 1.00e+0 A.2.5.1
V4058 2203T>G missense_variant S S735A 1.00e+0 A.2.5.1
V7507 12550C>T synonymous_variant ORF1ab_pp1a L4184L -7.06e-1 A.2.5.1
V9002 2880C>T synonymous_variant S N960N 1.00e+0 A.2.5.1
V3608 284C>T missense_variant S T95I 7.03e-1 AE.1
V3623 394G>C missense_variant S E132Q 1.00e+0 AE.1
V3727 632_634delATT disruptive_inframe_deletion S N211_L212delinsI 1.00e+0 AE.1
V3909 1450G>A missense_variant S E484K 1.00e+0 AE.1
V3927 1501A>T missense_variant S N501Y 1.00e+0 AE.1
V4663 26C>T missense_variant E T9I 1.00e+0 AE.1
V4732 85C>T missense_variant M L29F 7.03e-1 AE.1
V5026 43G>A missense_variant ORF7b A15T 1.00e+0 AE.1
V5243 -2A>T upstream_gene_variant N None 1.00e+0 AE.1
V9396 12C>T synonymous_variant ORF6 L4L 1.00e+0 AE.1
V1879 8788G>T missense_variant ORF1ab_pp1a V2930L 1.00e+0 AY.19
V1954 9446C>T missense_variant ORF1ab_pp1a S3149F 1.00e+0 AY.19
V7027 8721C>T synonymous_variant ORF1ab_pp1a D2907D 7.06e-1 AY.19
V7125 9537G>T synonymous_variant ORF1ab_pp1a A3179A 1.00e+0 AY.19
V2606 14267C>T missense_variant ORF1ab_pp1ab S4756F 1.00e+0 AY.25.1.1
V5705 68C>T missense_variant ORF10 S23F 1.00e+0 AY.4.1
V1982 9764C>T missense_variant ORF1ab_pp1a T3255I -1.00e+0 AY.5.1
V3717 570G>T missense_variant S R190S 1.00e+0 AY.5.1
V4986 314C>T missense_variant ORF7a A105V 1.00e+0 AY.5.1
V5496 643G>T missense_variant N G215C -1.00e+0 AY.5.1
V6224 2484C>T synonymous_variant ORF1ab_pp1a D828D 1.00e+0 AY.5.1
V6380 3727C>T synonymous_variant ORF1ab_pp1a L1243L 1.00e+0 AY.5.1
V9485 348C>T synonymous_variant ORF7a L116L 1.00e+0 AY.5.1
V1548 6497C>T missense_variant ORF1ab_pp1a T2166I 7.04e-1 B.1.1.117
V2163 11023_11031delTCTGGTTTT conservative_inframe_deletion ORF1ab_pp1a S3675_F3677del 7.04e-1 B.1.1.117
V2897 16995G>T missense_variant ORF1ab_pp1ab E5665D 7.04e-1 B.1.1.117
V3717 570G>T missense_variant S R190S 1.00e+0 B.1.1.117
V377 925C>T missense_variant ORF1ab_pp1a P309S 1.00e+0 B.1.1.117
V3854 1224A>C missense_variant S R408S 1.00e+0 B.1.1.117
V3861 1251G>T missense_variant S K417N 1.00e+0 B.1.1.117
V3868 1320T>G missense_variant S N440K 1.00e+0 B.1.1.117
V3885 1355T>A missense_variant S L452Q 1.00e+0 B.1.1.117
V3896 1430G>A missense_variant S S477N 1.00e+0 B.1.1.117
V3900 1433C>A missense_variant S T478K 1.00e+0 B.1.1.117
V3911 1451A>C missense_variant S E484A 1.00e+0 B.1.1.117
V3922 1478A>G missense_variant S Q493R 1.00e+0 B.1.1.117
V3926 1493A>G missense_variant S Q498R 1.00e+0 B.1.1.117
V3927 1501A>T missense_variant S N501Y 7.04e-1 B.1.1.117
V3930 1513T>C missense_variant S Y505H 1.00e+0 B.1.1.117
V4617 757T>C missense_variant ORF3a S253P 1.00e+0 B.1.1.117
V4892 113G>T missense_variant ORF7a G38V 1.00e+0 B.1.1.117
V5187 274G>A missense_variant ORF8 E92K 1.00e+0 B.1.1.117
V5924 468T>C synonymous_variant ORF1ab_pp1a D156D 7.04e-1 B.1.1.117
V6224 2484C>T synonymous_variant ORF1ab_pp1a D828D 1.00e+0 B.1.1.117
V6691 6054A>G synonymous_variant ORF1ab_pp1a P2018P 1.00e+0 B.1.1.117
V6736 6348A>G synonymous_variant ORF1ab_pp1a V2116V 7.04e-1 B.1.1.117
V3530 52C>T missense_variant S L18F 7.05e-1 B.1.1.161
V3535 59C>A missense_variant S T20N 7.05e-1 B.1.1.161
V3551 76C>T missense_variant S P26S 7.05e-1 B.1.1.161
V6736 6348A>G synonymous_variant ORF1ab_pp1a V2116V 1.00e+0 B.1.1.161
V260 421_429delAAGTCATTT conservative_inframe_deletion ORF1ab_pp1a K141_F143del 1.00e+0 B.1.1.253
V5096 79C>T stop_gained ORF8 Q27* 1.00e+0 B.1.1.253
V2711 15392C>T missense_variant ORF1ab_pp1ab T5131I 8.65e-1 B.1.1.302
V2856 16750G>T missense_variant ORF1ab_pp1ab D5584Y 1.00e+0 B.1.1.302
V8519 20406G>T synonymous_variant ORF1ab_pp1ab A6802A 8.16e-1 B.1.1.302
V5914 411C>T synonymous_variant ORF1ab_pp1a G137G 1.00e+0 B.1.1.322
V8583 20952C>T synonymous_variant ORF1ab_pp1ab H6984H 1.00e+0 B.1.1.322
V9707 747A>G synonymous_variant N K249K 1.00e+0 B.1.1.322
V2239 11422C>T missense_variant ORF1ab_pp1a L3808F 8.93e-1 B.1.1.385
V2285 11816C>T missense_variant ORF1ab_pp1a A3939V 7.05e-1 B.1.1.389
V3588 215G>T missense_variant S G72V 1.00e+0 B.1.1.389
V7829 14973C>T synonymous_variant ORF1ab_pp1ab H4991H 7.05e-1 B.1.1.389
V8163 17535A>G synonymous_variant ORF1ab_pp1ab V5845V 1.00e+0 B.1.1.389
V8624 33C>T synonymous_variant S V11V 7.05e-1 B.1.1.389
V9120 3714C>T synonymous_variant S T1238T 1.00e+0 B.1.1.389
V4426 203G>T missense_variant ORF3a R68I 1.00e+0 B.1.1.391
V8944 2461C>T synonymous_variant S L821L 1.00e+0 B.1.1.391
V1507 6344G>T missense_variant ORF1ab_pp1a R2115I 1.00e+0 B.1.1.448
V1717 7813C>T missense_variant ORF1ab_pp1a P2605S 1.00e+0 B.1.1.448
V2143 10957G>T missense_variant ORF1ab_pp1a V3653F 1.00e+0 B.1.1.448
V2434 13091C>T missense_variant ORF1ab_pp1a T4364I 7.06e-1 B.1.1.448
V2553 13862G>A missense_variant ORF1ab_pp1ab S4621N 1.00e+0 B.1.1.448
V2789 16202C>T missense_variant ORF1ab_pp1ab P5401L 7.06e-1 B.1.1.448
V3808 916T>C missense_variant S F306L 1.00e+0 B.1.1.448
V3924 1480T>C missense_variant S S494P 1.00e+0 B.1.1.448
V4760 245T>C missense_variant M I82T 1.00e+0 B.1.1.448
V493 1345A>G missense_variant ORF1ab_pp1a N449D 1.00e+0 B.1.1.448
V5244 -1A>T upstream_gene_variant N None 7.06e-1 B.1.1.448
V5489 634G>T missense_variant N G212C 1.00e+0 B.1.1.448
V5980 822A>G synonymous_variant ORF1ab_pp1a V274V 1.00e+0 B.1.1.448
V6035 1206C>T synonymous_variant ORF1ab_pp1a R402R 7.06e-1 B.1.1.448
V7084 9165C>T synonymous_variant ORF1ab_pp1a I3055I 1.00e+0 B.1.1.448
V7307 10959C>T synonymous_variant ORF1ab_pp1a V3653V 7.06e-1 B.1.1.448
V8040 16653G>A synonymous_variant ORF1ab_pp1ab L5551L 1.00e+0 B.1.1.448
V812 2704A>G missense_variant ORF1ab_pp1a M902V 1.00e+0 B.1.1.448
V1611 6868G>A missense_variant ORF1ab_pp1a V2290I 1.00e+0 B.1.1.48
V5672 -8C>T upstream_gene_variant ORF10 None 1.00e+0 B.1.164
V97 -25C>T upstream_gene_variant ORF1ab_pp1a None -7.02e-1 B.1.164
V9025 3123T>C synonymous_variant S D1041D 1.00e+0 B.1.177.55
V7652 13690T>C synonymous_variant ORF1ab_pp1ab L4564L 7.05e-1 B.1.177.85
V6833 7155C>T synonymous_variant ORF1ab_pp1a I2385I 1.00e+0 B.1.237
V9445 153T>C synonymous_variant ORF7a D51D 1.00e+0 B.1.237
V7273 10605G>T synonymous_variant ORF1ab_pp1a L3535L 7.05e-1 B.1.301
V7762 14433C>T synonymous_variant ORF1ab_pp1ab F4811F 7.06e-1 B.1.336
V9025 3123T>C synonymous_variant S D1041D 1.00e+0 B.1.336
V7284 10716G>T synonymous_variant ORF1ab_pp1a V3572V 1.00e+0 B.1.503
V7684 13920C>T synonymous_variant ORF1ab_pp1ab T4640T 1.00e+0 B.1.503
V1319 5383A>C missense_variant ORF1ab_pp1a K1795Q 7.01e-1 B.1.566
V1442 6137C>T missense_variant ORF1ab_pp1a P2046L 1.00e+0 B.1.566
V1626 7034C>T missense_variant ORF1ab_pp1a A2345V 1.00e+0 B.1.566
V1879 8788G>T missense_variant ORF1ab_pp1a V2930L 1.00e+0 B.1.566
V2033 10136C>T missense_variant ORF1ab_pp1a A3379V 1.00e+0 B.1.566
V3628 412G>T missense_variant S D138Y 1.00e+0 B.1.566
V3900 1433C>A missense_variant S T478K 1.00e+0 B.1.566
V4573 604G>T missense_variant ORF3a V202L 1.00e+0 B.1.566
V4617 757T>C missense_variant ORF3a S253P 7.01e-1 B.1.566
V4760 245T>C missense_variant M I82T 1.00e+0 B.1.566
V4952 245T>C missense_variant ORF7a V82A 1.00e+0 B.1.566
V5049 119C>T missense_variant ORF7b T40I 1.00e+0 B.1.566
V5187 274G>A missense_variant ORF8 E92K 7.01e-1 B.1.566
V5341 188A>G missense_variant N D63G 1.00e+0 B.1.566
V5462 608G>T missense_variant N R203M 1.00e+0 B.1.566
V5496 643G>T missense_variant N G215C 1.00e+0 B.1.566
V5614 1129G>T missense_variant N D377Y 1.00e+0 B.1.566
V5777 *4358G>T downstream_gene_variant S None 1.00e+0 B.1.566
V5924 468T>C synonymous_variant ORF1ab_pp1a D156D 1.00e+0 B.1.566
V6691 6054A>G synonymous_variant ORF1ab_pp1a P2018P 1.00e+0 B.1.566
V74 -56G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.566
V9002 2880C>T synonymous_variant S N960N 1.00e+0 B.1.566
V2653 14762C>T missense_variant ORF1ab_pp1ab A4921V 1.00e+0 B.1.634
V2789 16202C>T missense_variant ORF1ab_pp1ab P5401L -7.06e-1 B.1.634
V3828 1042G>T missense_variant S A348S 1.00e+0 B.1.634
V4624 766_769delGTTA frameshift_variant ORF3a V256fs 1.00e+0 B.1.634
V5241 -3A>T upstream_gene_variant N None -7.06e-1 B.1.634
V5924 468T>C synonymous_variant ORF1ab_pp1a D156D 1.00e+0 B.1.634
V5971 729A>G synonymous_variant ORF1ab_pp1a E243E 7.06e-1 B.1.634
V8463 19860T>A synonymous_variant ORF1ab_pp1ab I6620I 1.00e+0 B.1.634
V9569 57A>G synonymous_variant N G19G 1.00e+0 B.1.634
V1357 5642C>T missense_variant ORF1ab_pp1a T1881I 9.08e-1 B.1.636
V4551 539C>T missense_variant ORF3a S180F 6.58e-1 B.1.636
V6651 5721C>T synonymous_variant ORF1ab_pp1a F1907F 6.57e-1 B.1.636
V1868 8711A>G missense_variant ORF1ab_pp1a E2904G 1.00e+0 B.52
V2190 11165A>G missense_variant ORF1ab_pp1a Y3722C 1.00e+0 B.52
V2730 15593C>T missense_variant ORF1ab_pp1ab T5198I 1.00e+0 B.52
V2819 16486C>T missense_variant ORF1ab_pp1ab P5496S 1.00e+0 B.52
V3034 17984C>T missense_variant ORF1ab_pp1ab P5995L 1.00e+0 B.52
V3969 1841A>G missense_variant S D614G 1.00e+0 B.52
V4675 89C>T missense_variant E T30I 1.00e+0 B.52
V5629 1152G>T missense_variant N Q384H 1.00e+0 B.52
V7088 9183C>T synonymous_variant ORF1ab_pp1a A3061A 1.00e+0 B.52
V1633 7095G>T missense_variant ORF1ab_pp1a M2365I 1.00e+0 BA.2.10.3
V3983 1891C>T missense_variant S P631S 1.00e+0 BS.1.1
V4704 -26T>C upstream_gene_variant M None 1.00e+0 BS.1.1
V1501 6313C>T missense_variant ORF1ab_pp1a L2105F 1.00e+0 C.37.1





Manual curation of mutation (3080C>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
3080C>T T1027I Emerging Variants of SARS-CoV-2 and Novel Therapeutics Against Coronavirus (COVID-19) StatPearls Publishing 2023 34033342
3080C>T T1027I Organ-specific genome diversity of replication-competent SARS-CoV-2 Nat Commun 2021 34785663
3080C>T T1027I Potential differentiation of successive SARS-CoV-2 mutations by RNA: DNA hybrid analyses Biophys Chem 2023 37030215