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The current mutation

ID: V1066
DNA: 3662C>T
Protein: S1221L
Position: 3927








COV2Var annotation categories







Summary information of mutation (3662C>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   3927
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 3662C>T
  Ref Seq: C
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: S1221L
  Protein 3-letter Mutation: Ser1221Leu

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 (3662C>T) across geographic regions, temporal trends, and lineages

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



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



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

Collection date Lineage Total lineage monthly counts Lineage-specific monthly counts Lineage-specific monthly frequency
2020-10 B.1.177.57 34 21 6.18e-1
2020-10 B.1.1.37 34 7 2.06e-1
2020-10 B.1.232 34 4 1.18e-1
2020-11 B.1.177.57 48 44 9.17e-1
2020-11 B.1.232 48 2 4.17e-2
2020-11 B.1.243 48 1 2.08e-2
2020-12 B.1.232 133 118 8.87e-1
2020-12 B.1.36 133 5 3.76e-2
2020-12 B.1.1.222 133 3 2.26e-2
2020-03 B.1 5 5 1.00e+0
2020-04 B.1 5 5 1.00e+0
2020-06 B.1 2 2 1.00e+0
2020-07 B.1.1.356 4 2 5.00e-1
2020-07 B.1.320 4 2 5.00e-1
2020-09 B.1.177.57 7 4 5.71e-1
2020-09 B.1.1.28 7 1 1.43e-1
2020-09 B.1.128 7 1 1.43e-1
2021-01 B.1.232 104 62 5.96e-1
2021-01 B.1.1.7 104 11 1.06e-1
2021-01 B.1.2 104 9 8.65e-2
2021-10 AY.4 66 13 1.97e-1
2021-10 AY.98.1 66 13 1.97e-1
2021-10 AY.47 66 7 1.06e-1
2021-11 AY.4 96 30 3.12e-1
2021-11 AY.103 96 9 9.38e-2
2021-11 AY.98.1 96 9 9.38e-2
2021-12 AY.4 79 20 2.53e-1
2021-12 AY.20 79 6 7.59e-2
2021-12 AY.25.1 79 5 6.33e-2
2021-02 B.1.232 55 23 4.18e-1
2021-02 B.1.1.7 55 6 1.09e-1
2021-02 B.1.2 55 6 1.09e-1
2021-03 B.1.1.7 98 72 7.35e-1
2021-03 B.1.351 98 8 8.16e-2
2021-03 B.1.234 98 5 5.10e-2
2021-04 B.1.1.7 109 83 7.61e-1
2021-04 B.1.351 109 19 1.74e-1
2021-04 B.1.429 109 3 2.75e-2
2021-05 B.1.1.7 92 64 6.96e-1
2021-05 B.1.351 92 19 2.07e-1
2021-05 P.1 92 3 3.26e-2
2021-06 B.1 28 18 6.43e-1
2021-06 AY.4 28 4 1.43e-1
2021-06 AY.5.2 28 2 7.14e-2
2021-07 AY.4 57 16 2.81e-1
2021-07 B.1.617.2 57 9 1.58e-1
2021-07 AY.122 57 7 1.23e-1
2021-08 AY.4 52 12 2.31e-1
2021-08 AY.122 52 9 1.73e-1
2021-08 B.1.617.2 52 6 1.15e-1
2021-09 AY.4 61 7 1.15e-1
2021-09 AY.125 61 6 9.84e-2
2021-09 AY.47 61 6 9.84e-2
2022-01 BA.1.1 102 34 3.33e-1
2022-01 BA.1.15 102 16 1.57e-1
2022-01 BA.1 102 13 1.27e-1
2022-10 BA.2.75.2 10900 1335 1.22e-1
2022-10 BN.1.3 10900 1301 1.19e-1
2022-10 BM.1.1.3 10900 772 7.08e-2
2022-11 BN.1.3 20059 3851 1.92e-1
2022-11 BN.1.2 20059 1939 9.67e-2
2022-11 CH.1.1.3 20059 1499 7.47e-2
2022-12 BN.1.3 31548 5334 1.69e-1
2022-12 CH.1.1.3 31548 5020 1.59e-1
2022-12 BN.1.2 31548 3782 1.20e-1
2022-02 BA.1.1 89 49 5.51e-1
2022-02 BA.2.10 89 8 8.99e-2
2022-02 BA.1 89 6 6.74e-2
2022-03 BA.2 102 50 4.90e-1
2022-03 BA.1.1 102 16 1.57e-1
2022-03 BA.2.10 102 12 1.18e-1
2022-04 BA.2 46 29 6.30e-1
2022-04 BN.1.3 46 2 4.35e-2
2022-04 BA.1 46 1 2.17e-2
2022-05 BA.2 55 40 7.27e-1
2022-05 BA.2.9 55 5 9.09e-2
2022-05 BA.2.75 55 3 5.45e-2
2022-06 BA.2.75 759 550 7.25e-1
2022-06 BA.2.75.3 759 67 8.83e-2
2022-06 BA.2.75.10 759 35 4.61e-2
2022-07 BA.2.75 3559 1762 4.95e-1
2022-07 BA.2.75.1 3559 589 1.65e-1
2022-07 BA.2.75.3 3559 426 1.20e-1
2022-08 BA.2.75.1 5581 1182 2.12e-1
2022-08 BA.2.75 5581 990 1.77e-1
2022-08 BA.2.75.2 5581 502 8.99e-2
2022-09 BA.2.75.2 7572 1355 1.79e-1
2022-09 BM.1.1.3 7572 693 9.15e-2
2022-09 BL.1 7572 568 7.50e-2
2023-01 CH.1.1.3 26429 5933 2.24e-1
2023-01 BN.1.3 26429 4041 1.53e-1
2023-01 BN.1.2 26429 3308 1.25e-1
2023-02 CH.1.1.3 7697 2293 2.98e-1
2023-02 CH.1.1.1 7697 1590 2.07e-1
2023-02 CH.1.1 7697 768 9.98e-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
V1066 B.1.177.57 2.09e-2 69 2020-6-2 2021-3-14
V1066 B.1.177.72 2.75e-2 8 2020-11-7 2021-4-12
V1066 B.1.232 1.01e-1 212 2020-4-6 2021-5-7
V1066 BA.2.75 9.61e-1 3688 2021-12-31 2023-2-15
V1066 BA.2.75.1 9.81e-1 2545 2022-1-1 2022-12-15
V1066 BA.2.75.10 9.91e-1 337 2022-6-8 2023-1-11
V1066 BA.2.75.2 9.80e-1 4085 2022-1-1 2023-2-2
V1066 BA.2.75.3 9.95e-1 833 2022-5-20 2022-12-5
V1066 BA.2.75.4 9.55e-1 644 2022-6-9 2023-2-10
V1066 BA.2.75.5 9.66e-1 1801 2022-7-1 2023-2-1
V1066 BA.2.75.6 9.00e-1 162 2022-6-16 2023-2-1
V1066 BA.2.75.7 9.67e-1 117 2022-6-23 2023-1-3
V1066 BA.2.75.8 9.86e-1 72 2022-8-27 2022-12-12
V1066 BA.2.75.9 1.00e+0 32 2022-7-25 2022-11-22
V1066 BL.1 9.83e-1 1953 2022-1-3 2023-2-13
V1066 BL.1.1 9.77e-1 43 2022-8-17 2022-11-28
V1066 BL.1.2 1.00e+0 15 2022-8-24 2022-10-31
V1066 BL.1.3 1.00e+0 35 2022-7-30 2023-1-13
V1066 BL.1.4 9.66e-1 57 2022-7-27 2022-12-12
V1066 BL.2 9.72e-1 636 2022-6-9 2023-1-30
V1066 BL.2.1 1.00e+0 7 2022-9-20 2022-10-12
V1066 BL.3 9.62e-1 204 2022-6-9 2022-10-5
V1066 BL.4 9.81e-1 261 2022-6-9 2023-1-13
V1066 BL.5 7.58e-1 25 2022-8-2 2022-11-19
V1066 BL.6 9.96e-1 229 2022-9-2 2023-2-7
V1066 BM.1 9.74e-1 229 2022-6-9 2022-12-12
V1066 BM.1.1 9.44e-1 473 2022-7-19 2023-2-14
V1066 BM.1.1.1 4.98e-1 569 2022-7-8 2023-2-20
V1066 BM.1.1.2 1.00e+0 19 2022-9-5 2022-11-14
V1066 BM.1.1.3 9.71e-1 2489 2022-1-4 2023-2-15
V1066 BM.1.1.4 1.00e+0 112 2022-10-11 2023-2-21
V1066 BM.1.1.5 9.29e-1 78 2022-9-15 2023-2-10
V1066 BM.2 9.20e-1 311 2022-6-18 2023-2-20
V1066 BM.2.1 8.89e-1 104 2022-7-27 2023-1-31
V1066 BM.2.2 1.00e+0 8 2022-9-10 2022-11-7
V1066 BM.2.3 1.00e+0 11 2022-7-18 2022-11-11
V1066 BM.3 9.68e-1 30 2022-6-23 2022-9-19
V1066 BM.4 9.84e-1 61 2022-6-20 2023-2-21
V1066 BM.4.1 9.71e-1 133 2022-7-15 2023-2-16
V1066 BM.4.1.1 9.75e-1 1149 2022-7-20 2023-2-17
V1066 BM.5 1.00e+0 38 2022-7-13 2022-11-4
V1066 BM.6 1.00e+0 13 2022-6-13 2022-10-4
V1066 BN.1 9.69e-1 3506 2022-7-27 2023-2-21
V1066 BN.1.1 9.83e-1 906 2022-7-27 2023-2-15
V1066 BN.1.1.1 9.96e-1 483 2022-1-7 2023-2-21
V1066 BN.1.2 9.76e-1 9953 2022-1-24 2023-2-21
V1066 BN.1.2.1 9.65e-1 960 2022-9-21 2023-2-20
V1066 BN.1.3 9.71e-1 15352 2022-1-24 2023-2-23
V1066 BN.1.3.1 9.28e-1 4816 2022-3-11 2023-2-21
V1066 BN.1.3.2 1.00e+0 385 2022-11-7 2023-2-18
V1066 BN.1.3.3 9.88e-1 326 2022-8-1 2023-2-22
V1066 BN.1.3.4 9.83e-1 58 2022-10-9 2023-2-10
V1066 BN.1.4 9.66e-1 3922 2022-1-30 2023-2-23
V1066 BN.1.4.1 9.42e-1 163 2022-9-21 2023-2-18
V1066 BN.1.5 9.64e-1 3713 2022-2-7 2023-2-21
V1066 BN.1.5.1 1.00e+0 89 2022-10-24 2023-1-30
V1066 BN.1.6 9.90e-1 96 2022-9-21 2023-2-17
V1066 BN.1.7 9.34e-1 748 2022-9-14 2023-2-20
V1066 BN.1.8 9.82e-1 445 2022-8-24 2023-2-11
V1066 BN.1.9 9.70e-1 1025 2022-1-24 2023-2-22
V1066 BN.2 9.77e-1 173 2022-7-10 2023-1-31
V1066 BN.2.1 9.79e-1 47 2022-8-4 2023-1-30
V1066 BN.3 9.47e-1 90 2022-3-11 2023-2-10
V1066 BN.3.1 9.84e-1 1076 2022-9-21 2023-2-22
V1066 BN.4 9.40e-1 47 2022-8-23 2023-1-13
V1066 BN.5 9.68e-1 362 2022-1-31 2023-1-18
V1066 BN.6 9.73e-1 327 2022-6-25 2023-2-13
V1066 BR.1 9.79e-1 568 2022-1-20 2023-2-3
V1066 BR.1.1 1.00e+0 42 2022-9-11 2023-2-13
V1066 BR.1.2 9.80e-1 242 2022-9-15 2023-2-10
V1066 BR.2 9.51e-1 713 2022-8-29 2023-2-21
V1066 BR.2.1 9.48e-1 4721 2022-1-11 2023-2-22
V1066 BR.3 9.55e-1 342 2022-8-16 2023-2-14
V1066 BR.4 9.63e-1 78 2022-7-18 2023-1-5
V1066 BY.1 9.45e-1 1277 2022-1-1 2023-2-20
V1066 BY.1.1 6.00e-1 9 2022-8-22 2023-2-5
V1066 BY.1.1.1 9.44e-1 152 2022-9-13 2023-2-21
V1066 BY.1.2 9.81e-1 105 2022-8-20 2023-1-6
V1066 BY.1.2.1 1.00e+0 14 2022-9-19 2022-10-18
V1066 CA.1 8.71e-1 359 2022-8-14 2023-2-8
V1066 CA.2 9.60e-1 95 2022-7-25 2022-12-5
V1066 CA.3 9.60e-1 714 2022-5-8 2023-2-14
V1066 CA.3.1 9.93e-1 305 2022-9-28 2023-2-14
V1066 CA.4 9.79e-1 46 2022-8-23 2023-1-11
V1066 CA.5 9.62e-1 231 2022-8-24 2023-2-3
V1066 CA.6 1.00e+0 77 2022-8-6 2022-12-12
V1066 CA.7 9.65e-1 642 2022-9-27 2023-2-15
V1066 CB.1 8.98e-1 351 2021-12-21 2023-2-22
V1066 CH.1 1.00e+0 280 2022-8-17 2023-2-20
V1066 CH.1.1 9.73e-1 3691 2022-7-27 2023-2-23
V1066 CH.1.1.1 9.60e-1 5984 2022-10-15 2023-2-22
V1066 CH.1.1.2 9.54e-1 1326 2022-10-5 2023-2-23
V1066 CH.1.1.3 9.66e-1 14931 2022-1-9 2023-2-23
V1066 CH.1.1.4 9.67e-1 266 2022-7-28 2023-2-20
V1066 CH.1.1.5 9.94e-1 482 2022-11-9 2023-2-22
V1066 CH.2 1.00e+0 30 2022-8-11 2022-11-4
V1066 CH.3 9.73e-1 36 2022-9-4 2023-2-5
V1066 CH.3.1 3.27e-1 17 2022-11-8 2023-1-24
V1066 CJ.1 9.63e-1 1017 2022-9-6 2023-2-21
V1066 CJ.1.1 8.79e-1 102 2022-10-12 2023-2-17
V1066 CV.1 9.69e-1 467 2022-9-16 2023-2-17
V1066 CV.2 9.90e-1 97 2022-10-23 2023-1-23
V1066 DS.1 9.80e-1 100 2022-12-2 2023-2-17
V1066 XBB.3 1.82e-2 18 2022-9-2 2023-2-9
V1066 XBD 9.67e-1 290 2022-8-25 2023-2-7
V1066 XBK 9.74e-1 641 2022-1-11 2023-2-22
V1066 XBL 9.79e-1 92 2022-11-24 2023-2-22






Examining mutation (3662C>T) found in abundant sequences of non-human animal hosts

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

Animal host Lineage Source region Collection date Accession ID




Association between mutation (3662C>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 -1.60e+0 5.91e-1 -2.71e+0 6.82e-3 Decrease
Deceased -5.80e-1 4.77e-1 -1.21e+0 2.25e-1 Decrease
Homebound 7.56e-2 3.54e-1 2.13e-1 8.31e-1 Increase
Hospitalized -5.73e-1 2.44e-1 -2.35e+0 1.89e-2 Decrease
Mild 3.08e+0 8.70e-1 3.54e+0 4.06e-4 Increase
Recovered 1.65e+0 6.97e-1 2.37e+0 1.78e-2 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 3.16e-1 1.27e-1 2.48e+0 1.30e-2 Increase
18-39 5.86e-2 4.96e-2 1.18e+0 2.38e-1 Increase
40-64 -7.44e-3 4.86e-2 -1.53e-1 8.78e-1 Decrease
65-84 1.97e-2 6.15e-2 3.21e-1 7.49e-1 Increase
>=85 -7.45e-2 1.11e-1 -6.74e-1 5.00e-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 1.15e-1 4.72e-2 2.43e+0 1.51e-2 Increase





Investigating natural selection at mutation (3662C>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

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

Protein name Protein start Protein end Protein length Site Alpha Beta P-value Lineage Method
nsp3 2720 8554 1945 403 53.67 0.00 4.00e-2 BA.2.6 FEL
nsp3 2720 8554 1945 403 56.12 0.00 3.00e-2 BA.5.2.35 FEL
nsp3 2720 8554 1945 403 166.03 0.00 3.00e-2 BF.7.8 FEL
nsp3 2720 8554 1945 403 61.05 0.00 5.00e-2 BQ.1.25 FEL
nsp3 2720 8554 1945 403 37.37 0.00 4.00e-2 C.36 FEL
nsp3 2720 8554 1945 403 37.37 0.00 4.00e-2 AY.104 FEL
nsp3 2720 8554 1945 403 12.28 0.00 4.00e-2 AY.106 FEL
nsp3 2720 8554 1945 403 18.89 0.00 4.00e-2 AY.34.1 FEL
nsp3 2720 8554 1945 403 20.20 0.00 4.00e-2 AY.36.1 FEL
nsp3 2720 8554 1945 403 88.02 0.00 3.00e-2 B.1.1.10 FEL
nsp3 2720 8554 1945 403 5.40 0.00 5.00e-2 B.1.617.2 FEL
nsp3 2720 8554 1945 403 11.75 0.00 5.00e-2 BA.1.17.2 FEL
nsp3 2720 8554 1945 403 14.93 0.00 5.00e-2 BA.2 FEL
nsp3 2720 8554 1945 403 10.05 0.00 5.00e-2 BA.4.1 FEL
nsp3 2720 8554 1945 403 18.73 0.00 0.00e+0 BA.4.6 FEL
nsp3 2720 8554 1945 403 10.60 0.00 5.00e-2 BF.5 FEL
nsp3 2720 8554 1945 403 10.05 0.00 5.00e-2 BF.7 FEL
nsp3 2720 8554 1945 403 10.81 0.00 5.00e-2 AY.102 FEL
nsp3 2720 8554 1945 403 12.56 0.00 1.00e-2 AY.112 FEL
nsp3 2720 8554 1945 403 10.46 0.00 5.00e-2 AY.120 FEL
nsp3 2720 8554 1945 403 11.75 0.00 5.00e-2 AY.126 FEL
nsp3 2720 8554 1945 403 18.89 0.00 4.00e-2 AY.14 FEL
nsp3 2720 8554 1945 403 10.39 0.00 4.00e-2 B.1.1.7 FEL
nsp3 2720 8554 1945 403 2113.11 0.00 3.00e-2 B.10 FEL
nsp3 2720 8554 1945 403 145.04 0.00 2.00e-2 B.1.1.241 FEL
nsp3 2720 8554 1945 403 8850.79 0.00 1.00e-2 B.1.1.410 FEL

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

Protein name Protein start Protein end Protein length Site Prob[alpha>beta] Prob[alpha<beta] Lineage Method
nsp3 2720 8554 1945 403 1.00e-2 9.60e-1 BN.1.3.1 FUBAR
nsp3 2720 8554 1945 403 2.00e-2 9.60e-1 BN.1.4 FUBAR
nsp3 2720 8554 1945 403 9.80e-1 1.00e-2 BA.4.6 FUBAR




Alterations in protein physicochemical properties induced by mutation (3662C>T)

Understanding the alterations in protein physicochemical properties can reveal the evolutionary processes and adaptive changes of viruses
Note: ProtParam software was used for the analysis of physicochemical properties. Significant change threshold: A change exceeding 10% compared to the reference is considered a significant change. "GRAVY" is an abbreviation for "grand average of hydropathicity".

Group Protein name Molecular weight Theoretical PI Extinction coefficients Aliphatic index GRAVY
Mutation ORF1ab_pp1a 490015 6.04 543550 89.08 -0.022
Reference ORF1ab_pp1a 489988.91 6.04 543550 88.99 -0.023




Alterations in protein stability induced by mutation (3662C>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
S1221L ORF1ab_pp1a Point 1221 -0.84 Decrease 7 25 Environment
S1221L ORF1ab_pp1a Point 1221 -0.76 Decrease 7.4 37 Internal




Impact on protein function induced by mutation (3662C>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
S1221L ORF1ab_pp1a Point 0.063 Loss of Phosphorylation at S1221 (Pr = 0.53 | P = 3.4e-03)
Loss of Strand (Pr = 0.25 | P = 0.08)
Gain of SUMOylation at K1219 (Pr = 0.23 | P = 0.02)
Gain of Acetylation at K1219 (Pr = 0.21 | P = 0.03)
Loss of ADP-ribosylation at R1225 (Pr = 0.17 | P = 0.09)
Altered Coiled_coil (Pr = 0.13 | P = 0.03)
Altered Cytoplasmic_loop (Pr = 0.10 | P = 0.04)




Exploring mutation (3662C>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 (3662C>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
S1221L ORF1ab_pp1a 3927 Pepsin (pH1.3) ESKPLVEQRK (pos: 1220)
 NA
S1221L ORF1ab_pp1a 3927 Proteinase K SKPLVEQRKQ (pos: 1221)
 NA
S1221L ORF1ab_pp1a 3927 Thermolysin ESKPLVEQRK (pos: 1220)
 NA
S1221L ORF1ab_pp1a 3927 Chymotrypsin-low specificity SKPLVEQRKQ (pos: 1221)
 NA
S1221L ORF1ab_pp1a 3927 Pepsin (pH>2) ESKPLVEQRK (pos: 1220)
 NA




Impact of spike protein mutation (3662C>T) on antigenicity and immunogenicity

Investigating the impact of mutations on antigenicity and immunogenicity carries important implications for vaccine design and our understanding of immune responses.
Note: An absolute change greater than 0.0102 (three times the median across sites) in antigenicity score is considered significant. An absolute changegreater than 0.2754 (three times the median across sites) in immunogenicity score is considered significant. The VaxiJen tool was utilized for antigenicity analysis. The IEDB tool was used for immunogenicity analysis. Antigens with a prediction score of more than 0.4 for this tool are considered candidate antigens. MHC I immunogenicity score >0, indicating a higher probability to stimulate an immune response.

Group Protein name Protein region Antigenicity score Immunogenicity score




Impact of mutation (3662C>T) on viral transmissibility by the affinity between RBD and ACE2 receptor

Unraveling the impact of mutations on the interaction between the receptor binding domain (RBD) and ACE2 receptor using deep mutational scanning (DMS) experimental data to gain insights into their effects on viral transmissibility.
Note: The ΔBinding affinity represents the disparity between the binding affinity of a mutation and the reference binding affinity. A positive Δbinding affinity value (Δlog10(KD,app) > 0) signifies an increased affinity between RBD and ACE2 receptor due to the mutation. Conversely, a negative value (Δlog10(KD,app) < 0) indicates a reduced affinity between RBD and ACE2 receptor caused by the mutation. A p-value smaller than 0.05 indicates significance. "Ave mut bind" represents the average binding affinity of this mutation. "Ave ref bind" refers to the average binding affinity at a site without any mutation (reference binding affinity).

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Mutation Protein name Protein region Mutation Position Ave mut bind Ave ref bind ΔBinding affinity P-value Image


The interface between the receptor binding domain (RBD) and ACE2 receptor is depicted in the crystal structure 6JM0.
Note: The structure 6M0J encompasses the RBD range of 333 to 526. The binding sites (403-406, 408, 417, 439, 445-447, 449, 453, 455-456, 473-478, 484-498, and 500-506) on the RBD that interface with ACE2 are indicated in magenta. The binding sites on the RBD that have been identified through the interface footprints experiment. The ACE2 binding sites within the interface are shown in cyan, representing residues within 5Å proximity to the RBD binding sites. The mutation within the RBD range of 333 to 526 is depicted in red.

        Show as:

        Show interface residues:





Impact of mutation (3662C>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 (3662C>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
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 8.16e-1 BA.2.3
V617 1829C>T missense_variant ORF1ab_pp1a S610L 7.83e-1 AY.125
V8600 21033C>T synonymous_variant ORF1ab_pp1ab G7011G 8.36e-1 AY.47
V3294 19783A>G missense_variant ORF1ab_pp1ab I6595V 1.00e+0 AY.98
V3818 1015G>C missense_variant S G339R 6.32e-1 B.1.1
V4664 31A>G missense_variant E T11A 6.32e-1 B.1.1
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 7.07e-1 BF.7
V2343 12275C>T missense_variant ORF1ab_pp1a A4092V 1.00e+0 A.2.5
V6461 4317C>T synonymous_variant ORF1ab_pp1a N1439N 6.32e-1 A.2.5
V4227 3500G>T missense_variant S G1167V 7.07e-1 AY.109
V820 2762A>G missense_variant ORF1ab_pp1a Y921C 7.07e-1 AY.109
V8317 18624C>T synonymous_variant ORF1ab_pp1ab H6208H 7.07e-1 AY.109
V1422 6071C>T missense_variant ORF1ab_pp1a S2024L 7.07e-1 AY.110
V6292 2988C>T synonymous_variant ORF1ab_pp1a D996D 7.07e-1 AY.110
V6325 3228T>C synonymous_variant ORF1ab_pp1a N1076N 7.07e-1 AY.110
V6596 5274G>A synonymous_variant ORF1ab_pp1a Q1758Q 8.16e-1 AY.116.1
V6029 1176C>T synonymous_variant ORF1ab_pp1a G392G 7.07e-1 AY.117
V8294 18486T>C synonymous_variant ORF1ab_pp1ab Y6162Y 1.00e+0 AY.24
V4164 3193G>T missense_variant S V1065L 9.43e-1 AY.27
V4695 217C>T missense_variant E L73F 6.17e-1 AY.27
V8137 17358A>G synonymous_variant ORF1ab_pp1ab K5786K 1.00e+0 AY.27
V8705 558C>T synonymous_variant S F186F 7.07e-1 AY.27
V4804 25G>T missense_variant ORF6 V9F 1.00e+0 AY.38
V7863 15222A>G synonymous_variant ORF1ab_pp1ab S5074S 1.00e+0 AY.45
V4464 298G>A missense_variant ORF3a G100S 1.00e+0 AY.54
V2855 16748C>T missense_variant ORF1ab_pp1ab S5583L 1.00e+0 AY.57
V7333 11214C>T synonymous_variant ORF1ab_pp1a I3738I 7.07e-1 AY.57
V2714 15408G>T missense_variant ORF1ab_pp1ab E5136D 1.00e+0 AY.63
V3755 727_732delGCTTTA conservative_inframe_deletion S A243_L244del 7.07e-1 AY.65
V3757 727G>C missense_variant S A243P 1.00e+0 AY.65
V440 1174G>A missense_variant ORF1ab_pp1a G392S 7.07e-1 AY.65
V5628 1148C>T missense_variant N P383L 1.00e+0 AY.73
V2347 12304G>A missense_variant ORF1ab_pp1a V4102I 7.07e-1 AY.95
V3686 531G>T missense_variant S M177I 1.00e+0 AY.95
V4546 524C>T missense_variant ORF3a T175I 1.00e+0 AY.95
V9138 21C>T synonymous_variant ORF3a I7I 7.07e-1 AY.95
V8132 17286C>T synonymous_variant ORF1ab_pp1ab L5762L 7.09e-1 AY.98.1
V8317 18624C>T synonymous_variant ORF1ab_pp1ab H6208H 8.93e-1 AY.98.1
V8868 1872T>C synonymous_variant S I624I 9.44e-1 AY.98.1
V4500 379C>T missense_variant ORF3a L127F 7.07e-1 AY.99.2
V2156 11007G>T missense_variant ORF1ab_pp1a M3669I 7.07e-1 B.1.1.170
V2036 10183C>T missense_variant ORF1ab_pp1a P3395S 6.54e-1 B.1.1.222
V3090 18304C>T missense_variant ORF1ab_pp1ab L6102F 1.00e+0 B.1.1.232
V3642 431A>C missense_variant S Y144S 1.00e+0 B.1.1.232
V3648 436C>A missense_variant S H146N 1.00e+0 B.1.1.232
V5756 *4346C>T downstream_gene_variant S None 7.07e-1 B.1.1.25
V5804 *4380G>T downstream_gene_variant S None 1.00e+0 B.1.1.25
V7019 8652C>T synonymous_variant ORF1ab_pp1a F2884F 7.07e-1 B.1.1.25
V7513 12567G>A synonymous_variant ORF1ab_pp1a Q4189Q 7.07e-1 B.1.1.28
V7079 9126C>T synonymous_variant ORF1ab_pp1a D3042D 7.07e-1 B.1.1.519
V8801 1317C>T synonymous_variant S N439N 1.00e+0 B.1.177.35
V550 1619C>T missense_variant ORF1ab_pp1a A540V 1.00e+0 B.1.177.86
V9093 3522T>C synonymous_variant S A1174A 1.00e+0 B.1.177.86
V8678 336G>T synonymous_variant S S112S 7.07e-1 B.1.221
V1352 5584C>T missense_variant ORF1ab_pp1a P1862S -6.54e-1 B.1.232
V1406 6020C>T missense_variant ORF1ab_pp1a T2007I -6.39e-1 B.1.232
V2934 17297G>A missense_variant ORF1ab_pp1ab R5766Q 9.68e-1 B.1.232
V3823 1037G>A missense_variant S R346K 9.37e-1 B.1.232
V4460 293C>T missense_variant ORF3a A98V 9.87e-1 B.1.232
V5041 97G>T stop_gained ORF7b E33* 9.44e-1 B.1.232
V518 1465G>A missense_variant ORF1ab_pp1a E489K 9.87e-1 B.1.232
V5943 576C>T synonymous_variant ORF1ab_pp1a G192G 9.90e-1 B.1.232
V6753 6441C>T synonymous_variant ORF1ab_pp1a N2147N -6.25e-1 B.1.232
V7550 12850C>T synonymous_variant ORF1ab_pp1a L4284L 9.44e-1 B.1.232
V7941 15828C>T synonymous_variant ORF1ab_pp1ab Y5276Y -6.60e-1 B.1.232
V8466 19884C>T synonymous_variant ORF1ab_pp1ab F6628F 9.63e-1 B.1.232
V9304 159C>T synonymous_variant M F53F 9.37e-1 B.1.232
V9561 18C>T synonymous_variant N P6P -6.53e-1 B.1.232
V7729 14227C>T synonymous_variant ORF1ab_pp1ab L4743L 8.02e-1 B.1.234
V8334 18762T>C synonymous_variant ORF1ab_pp1ab L6254L 8.66e-1 B.1.234
V1145 4210C>T missense_variant ORF1ab_pp1a R1404C 1.00e+0 B.1.320
V3138 18664C>T missense_variant ORF1ab_pp1ab P6222S 1.00e+0 B.1.320
V5481 626G>T missense_variant N R209I 1.00e+0 B.1.320
V2032 10112C>T missense_variant ORF1ab_pp1a P3371L 6.13e-1 B.1.351
V3564 152C>T missense_variant S T51I 6.59e-1 B.1.351
V7888 15450C>T synonymous_variant ORF1ab_pp1ab L5150L 7.93e-1 B.1.351
V8295 18492G>A synonymous_variant ORF1ab_pp1ab P6164P 8.67e-1 B.1.351
V1354 5621C>T missense_variant ORF1ab_pp1a T1874I 1.00e+0 B.1.36.22
V1437 6108G>T missense_variant ORF1ab_pp1a M2036I 1.00e+0 B.1.36.22
V198 257_259delTTG disruptive_inframe_deletion ORF1ab_pp1a V86del 7.07e-1 B.1.36.22
V2430 13061C>T missense_variant ORF1ab_pp1a T4354I 1.00e+0 B.1.36.22
V3896 1430G>A missense_variant S S477N 8.16e-1 B.1.36.22
V3949 1708G>T missense_variant S A570S 1.00e+0 B.1.36.22
V4130 2806G>C missense_variant S D936H 1.00e+0 B.1.36.22
V4403 164T>G missense_variant ORF3a V55G 6.31e-1 B.1.36.22
V7868 15279G>A synonymous_variant ORF1ab_pp1ab T5093T 1.00e+0 B.1.36.22
V7947 15909C>T synonymous_variant ORF1ab_pp1ab N5303N 1.00e+0 B.1.36.22
V8194 17796C>T synonymous_variant ORF1ab_pp1ab L5932L 1.00e+0 B.1.36.22
V3949 1708G>T missense_variant S A570S 9.66e-1 B.1.36
V4130 2806G>C missense_variant S D936H 6.41e-1 B.1.36
V4087 2452A>G missense_variant S I818V 1.00e+0 B.1.398
V4389 146G>T missense_variant ORF3a G49V 1.00e+0 B.1.398
V7348 11355C>T synonymous_variant ORF1ab_pp1a F3785F 1.00e+0 B.1.398
V8116 17175C>T synonymous_variant ORF1ab_pp1ab D5725D 1.00e+0 B.1.398
V880 2974G>T missense_variant ORF1ab_pp1a D992Y 7.06e-1 B.1.398
V631 1879G>T missense_variant ORF1ab_pp1a V627F 7.07e-1 B.1.525
V1475 6236C>T missense_variant ORF1ab_pp1a P2079L 7.07e-1 B.1.560
V2211 11256G>T missense_variant ORF1ab_pp1a M3752I 1.00e+0 B.1.560
V5912 399C>T synonymous_variant ORF1ab_pp1a G133G 1.00e+0 B.1.560
V7684 13920C>T synonymous_variant ORF1ab_pp1ab T4640T 8.16e-1 B.1.560
V8694 447C>T synonymous_variant S N149N 8.16e-1 B.1.560
V8884 1977A>T synonymous_variant S S659S 7.07e-1 B.1.560
V1152 4286C>T missense_variant ORF1ab_pp1a T1429I 7.07e-1 BA.1.1.13
V3118 18524C>T missense_variant ORF1ab_pp1ab T6175I 7.07e-1 BA.1.13.1
V4378 130G>A missense_variant ORF3a G44R 1.00e+0 BA.1.14
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 8.85e-1 BA.2.10.1
V6241 2598A>G synonymous_variant ORF1ab_pp1a T866T 7.90e-1 BA.2.10.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.73e-1 BA.2.10.1
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 7.49e-1 BA.2.10.1
V8399 19290C>T synonymous_variant ORF1ab_pp1ab G6430G 7.50e-1 BA.2.10.1
V9180 246C>T synonymous_variant ORF3a N82N 8.12e-1 BA.2.10.1
V1030 3526G>A missense_variant ORF1ab_pp1a A1176T 7.07e-1 BA.2.12
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 7.07e-1 BA.2.12
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 7.07e-1 BA.2.12
V2132 10881G>T missense_variant ORF1ab_pp1a M3627I 7.07e-1 BA.2.12
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 1.00e+0 BA.2.12
V3405 20477A>G missense_variant ORF1ab_pp1ab Q6826R 7.07e-1 BA.2.12
V3662 454T>C missense_variant S W152R 7.07e-1 BA.2.12
V3724 628A>G missense_variant S I210V 7.07e-1 BA.2.12
V4010 2025G>C missense_variant S Q675H 7.07e-1 BA.2.12
V4664 31A>G missense_variant E T11A 6.32e-1 BA.2.12
V4825 122C>T missense_variant ORF6 S41F 7.07e-1 BA.2.12
V561 1648C>T missense_variant ORF1ab_pp1a R550C 7.07e-1 BA.2.12
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.07e-1 BA.2.12
V7468 12150C>T synonymous_variant ORF1ab_pp1a N4050N 7.07e-1 BA.2.12
V7781 14541C>T synonymous_variant ORF1ab_pp1ab Y4847Y 7.07e-1 BA.2.12
V8634 120C>T synonymous_variant S D40D 7.07e-1 BA.2.12
V1420 6064T>C missense_variant ORF1ab_pp1a S2022P 1.00e+0 BA.2.21
V1460 6194A>G missense_variant ORF1ab_pp1a N2065S 8.66e-1 BA.2.23.1
V1980 9731C>T missense_variant ORF1ab_pp1a S3244L 8.66e-1 BA.2.23.1
V2329 12194C>T missense_variant ORF1ab_pp1a T4065I 6.01e-1 BA.2.23.1
V4866 41C>T missense_variant ORF7a T14I 6.31e-1 BA.2.23.1
V8584 20955C>T synonymous_variant ORF1ab_pp1ab F6985F 6.01e-1 BA.2.23.1
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 1.00e+0 BA.2.23
V2989 17724G>T missense_variant ORF1ab_pp1ab K5908N 1.00e+0 BA.2.23
V3652 439A>G missense_variant S K147E 1.00e+0 BA.2.23
V3662 454T>C missense_variant S W152R 7.07e-1 BA.2.23
V3724 628A>G missense_variant S I210V 7.07e-1 BA.2.23
V3784 769G>A missense_variant S G257S 7.07e-1 BA.2.23
V3818 1015G>C missense_variant S G339R 1.00e+0 BA.2.23
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BA.2.23
V5386 422C>T missense_variant N T141I 1.00e+0 BA.2.3.12
V9523 108G>T synonymous_variant ORF8 P36P 1.00e+0 BA.2.3.14
V4664 31A>G missense_variant E T11A 1.00e+0 BA.2.38.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BA.2.38.1
V1552 6542C>T missense_variant ORF1ab_pp1a T2181I 7.07e-1 BA.2.38
V3793 782G>T missense_variant S G261V 1.00e+0 BA.2.65
V694 2168C>T missense_variant ORF1ab_pp1a S723F 7.07e-1 BA.2.65
V8305 18552G>T synonymous_variant ORF1ab_pp1ab L6184L 1.00e+0 BA.2.65
V6218 2439C>T synonymous_variant ORF1ab_pp1a F813F 7.49e-1 BA.2.74
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.10e-1 BA.2.75.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.17e-1 BA.2.75.2
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 6.10e-1 BA.2.75.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 6.69e-1 BA.2.75.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 6.19e-1 BA.2.75.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.56e-1 BA.2.75.5
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 6.00e-1 BA.2.75
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.22e-1 BA.2.75
V3752 719C>T missense_variant S T240I 7.07e-1 BA.2.76
V3818 1015G>C missense_variant S G339R 7.07e-1 BA.2.76
V8581 20943C>T synonymous_variant ORF1ab_pp1ab L6981L 1.00e+0 BA.4.1.1
V934 3164C>T missense_variant ORF1ab_pp1a T1055I 1.00e+0 BA.4.1.1
V9378 537C>T synonymous_variant M Y179Y 1.00e+0 BA.4.1.1
V1477 6239C>T missense_variant ORF1ab_pp1a A2080V 7.07e-1 BA.4.2
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 1.00e+0 BA.4.6.4
V5902 336C>T synonymous_variant ORF1ab_pp1a G112G 1.00e+0 BA.4.6.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BA.4.6.4
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 1.00e+0 BA.4.6.4
V66 -63C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 BA.4.6.4
V9176 222C>T synonymous_variant ORF3a S74S 7.07e-1 BA.4.6.4
V1428 6089C>T missense_variant ORF1ab_pp1a S2030L 1.00e+0 BA.5.1.12
V2271 11765A>G missense_variant ORF1ab_pp1a Q3922R 7.07e-1 BA.5.1.12
V3695 542G>A missense_variant S G181E 1.00e+0 BA.5.1.12
V5200 316G>T stop_gained ORF8 E106* 7.07e-1 BA.5.1.12
V8261 18237C>T synonymous_variant ORF1ab_pp1ab Y6079Y 1.00e+0 BA.5.1.12
V8381 19125T>C synonymous_variant ORF1ab_pp1ab S6375S 1.00e+0 BA.5.1.12
V8788 1236A>G synonymous_variant S P412P 1.00e+0 BA.5.1.12
V451 1204C>T missense_variant ORF1ab_pp1a R402C 7.07e-1 BA.5.11
V8431 19590C>T synonymous_variant ORF1ab_pp1ab D6530D 8.16e-1 BA.5.11
V585 1711G>T missense_variant ORF1ab_pp1a D571Y 8.66e-1 BA.5.2.20
V91 -34T>C upstream_gene_variant ORF1ab_pp1a None 8.66e-1 BA.5.2.20
V5380 401C>T missense_variant N A134V 7.29e-1 BA.5.2.47
V9012 2961T>C synonymous_variant S V987V 6.86e-1 BA.5.2.47
V6501 4632C>T synonymous_variant ORF1ab_pp1a F1544F 1.00e+0 BA.5.2.49
V5973 744C>T synonymous_variant ORF1ab_pp1a S248S 8.36e-1 BA.5.2.6
V1065 3661T>C missense_variant ORF1ab_pp1a S1221P 8.45e-1 BC.1
V1067 3664G>A missense_variant ORF1ab_pp1a V1222I 7.97e-1 BC.1
V2132 10881G>T missense_variant ORF1ab_pp1a M3627I 7.07e-1 BE.1.1.2
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 1.00e+0 BE.1.1.2
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 7.07e-1 BE.1.1.2
V5881 249T>C synonymous_variant ORF1ab_pp1a H83H 7.07e-1 BE.1.1.2
V6247 2637C>T synonymous_variant ORF1ab_pp1a V879V 7.07e-1 BE.1.1.2
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BE.1.1.2
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 1.00e+0 BE.1.1.2
V6827 7125C>A synonymous_variant ORF1ab_pp1a A2375A 7.07e-1 BE.1.1.2
V7030 8772T>C synonymous_variant ORF1ab_pp1a D2924D 7.07e-1 BE.1.1.2
V9742 900T>C synonymous_variant N H300H 7.07e-1 BE.1.1.2
V8177 17616A>G synonymous_variant ORF1ab_pp1ab Q5872Q 1.00e+0 BE.1
V7224 10206A>G synonymous_variant ORF1ab_pp1a S3402S 7.07e-1 BE.3
V3917 1457T>C missense_variant S F486S 1.00e+0 BF.15
V5293 71C>T missense_variant N T24I 1.00e+0 BF.15
V4058 2203T>G missense_variant S S735A 7.07e-1 BF.28
V5804 *4380G>T downstream_gene_variant S None 7.07e-1 BF.28
V8760 1017T>C synonymous_variant S G339G 7.07e-1 BF.28
V1414 6047C>T missense_variant ORF1ab_pp1a T2016I 8.16e-1 BF.7.15
V4535 512C>T missense_variant ORF3a S171L 7.07e-1 BF.7.15
V1911 9095C>T missense_variant ORF1ab_pp1a T3032I 1.00e+0 BF.7.5
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 1.00e+0 BF.7.5
V3818 1015G>C missense_variant S G339R 1.00e+0 BF.7.5
V9401 58A>C synonymous_variant ORF6 R20R 1.00e+0 BF.7.5
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 B
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.29e-1 BL.1
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 6.94e-1 BL.2
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 6.39e-1 BL.2
V4144 2862A>T missense_variant S Q954H 6.39e-1 BL.2
V4146 2907T>A missense_variant S N969K 7.13e-1 BL.2
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.24e-1 BL.2
V7888 15450C>T synonymous_variant ORF1ab_pp1ab L5150L 7.13e-1 BL.2
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 9.75e-1 BM.1.1.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.84e-1 BM.1.1.1
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 7.67e-1 BM.1.1.1
V6663 5805C>T synonymous_variant ORF1ab_pp1a I1935I -7.85e-1 BM.1.1.1
V6985 8427C>T synonymous_variant ORF1ab_pp1a Y2809Y -8.04e-1 BM.1.1.1
V915 3074T>C missense_variant ORF1ab_pp1a V1025A -7.79e-1 BM.1.1.1
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 6.09e-1 BM.1.1.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.84e-1 BM.1.1.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.04e-1 BM.1.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.66e-1 BM.4.1.1
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 6.14e-1 BN.1.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 6.24e-1 BN.1.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.01e-1 BN.1.2.1
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 7.40e-1 BN.1.2
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 7.32e-1 BN.1.2
V2037 10184C>A missense_variant ORF1ab_pp1a P3395H 6.29e-1 BN.1.2
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 6.42e-1 BN.1.2
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 6.66e-1 BN.1.2
V4144 2862A>T missense_variant S Q954H 7.05e-1 BN.1.2
V4146 2907T>A missense_variant S N969K 7.17e-1 BN.1.2
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.85e-1 BN.1.2
V7219 10182G>A synonymous_variant ORF1ab_pp1a R3394R 6.20e-1 BN.1.2
V7888 15450C>T synonymous_variant ORF1ab_pp1ab L5150L 6.70e-1 BN.1.2
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 6.87e-1 BN.1.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.85e-1 BN.1.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 6.22e-1 BN.1.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.24e-1 BN.1.5
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.18e-1 BN.1.7
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.33e-1 BN.1.9
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 6.01e-1 BN.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 6.89e-1 BN.1
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 6.32e-1 BN.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.28e-1 BN.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.00e-1 BN.3.1
V2154 11001G>T missense_variant ORF1ab_pp1a L3667F 1.00e+0 BQ.1.1.13
V8039 16651C>T synonymous_variant ORF1ab_pp1ab L5551L 7.07e-1 BQ.1.1.13
V9339 354T>C synonymous_variant M I118I 7.07e-1 BQ.1.1.13
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F 7.07e-1 BQ.1.1.15
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 1.00e+0 BQ.1.1.15
V2982 17695A>G missense_variant ORF1ab_pp1ab I5899V 1.00e+0 BQ.1.1.15
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BQ.1.1.15
V143 119C>T missense_variant ORF1ab_pp1a S40L 1.00e+0 BQ.1.1.16
V7795 14661C>T synonymous_variant ORF1ab_pp1ab V4887V 1.00e+0 BQ.1.1.16
V9712 771G>A synonymous_variant N K257K 6.61e-1 BQ.1.1.18
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 1.00e+0 BQ.1.11
V1742 7910C>T missense_variant ORF1ab_pp1a A2637V 1.00e+0 BQ.1.11
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F 1.00e+0 BQ.1.11
V2388 12589C>T missense_variant ORF1ab_pp1a P4197S 7.07e-1 BQ.1.11
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 1.00e+0 BQ.1.11
V3662 454T>C missense_variant S W152R 1.00e+0 BQ.1.11
V391 989C>T missense_variant ORF1ab_pp1a S330L 7.07e-1 BQ.1.11
V4176 3232G>T missense_variant S A1078S 7.07e-1 BQ.1.13.1
V6245 2616C>T synonymous_variant ORF1ab_pp1a A872A 7.07e-1 BQ.1.13.1
V6245 2616C>T synonymous_variant ORF1ab_pp1a A872A 6.71e-1 BQ.1.1.32
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F 1.00e+0 BQ.1.14
V2715 15415G>T missense_variant ORF1ab_pp1ab A5139S 1.00e+0 BQ.1.14
V3662 454T>C missense_variant S W152R 1.00e+0 BQ.1.14
V3675 471C>A missense_variant S F157L 1.00e+0 BQ.1.14
V4839 181G>C missense_variant ORF6 D61H 7.07e-1 BQ.1.14
V4841 182A>T missense_variant ORF6 D61V 7.07e-1 BQ.1.14
V5027 43G>T missense_variant ORF7b A15S 1.00e+0 BQ.1.14
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BQ.1.14
V6372 3612T>C synonymous_variant ORF1ab_pp1a A1204A 1.00e+0 BQ.1.14
V6926 7902T>C synonymous_variant ORF1ab_pp1a I2634I 1.00e+0 BQ.1.14
V9139 24C>T synonymous_variant ORF3a F8F 1.00e+0 BQ.1.14
V5410 497C>T missense_variant N T166I 1.00e+0 BQ.1.1.5
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 1.00e+0 BQ.1.16
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F 1.00e+0 BQ.1.16
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 1.00e+0 BQ.1.16
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 1.00e+0 BQ.1.16
V3662 454T>C missense_variant S W152R 1.00e+0 BQ.1.16
V3675 471C>A missense_variant S F157L 1.00e+0 BQ.1.16
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BQ.1.16
V7529 12687C>T synonymous_variant ORF1ab_pp1a Y4229Y 1.00e+0 BQ.1.16
V8521 20415G>T synonymous_variant ORF1ab_pp1ab P6805P 7.07e-1 BQ.1.16
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BQ.1.1.8
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 6.70e-1 BQ.1.1.8
V2364 12473C>T missense_variant ORF1ab_pp1a T4158I 8.45e-1 BQ.1.18
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 1.00e+0 BQ.1.24
V1394 5930C>T missense_variant ORF1ab_pp1a P1977L 1.00e+0 BQ.1.24
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 7.07e-1 BQ.1.24
V350 820G>T missense_variant ORF1ab_pp1a V274L 7.07e-1 BQ.1.24
V4604 686C>T missense_variant ORF3a T229I 7.07e-1 BQ.1.24
V4664 31A>G missense_variant E T11A 1.00e+0 BQ.1.24
V8178 17619C>T synonymous_variant ORF1ab_pp1ab T5873T 1.00e+0 BQ.1.24
V8799 1296C>T synonymous_variant S C432C 1.00e+0 BQ.1.24
V9139 24C>T synonymous_variant ORF3a F8F 7.07e-1 BQ.1.24
V205 274C>T missense_variant ORF1ab_pp1a L92F 1.00e+0 BQ.1.28
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F 7.07e-1 BQ.1.3
V6770 6618C>T synonymous_variant ORF1ab_pp1a V2206V 7.30e-1 BQ.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.78e-1 BR.1
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 8.22e-1 BR.2.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 7.00e-1 BR.2.1
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 6.92e-1 BR.2.1
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 7.70e-1 BR.2.1
V3724 628A>G missense_variant S I210V 6.18e-1 BR.2.1
V3735 638T>G missense_variant S V213G 6.16e-1 BR.2.1
V3784 769G>A missense_variant S G257S 6.78e-1 BR.2.1
V3818 1015G>C missense_variant S G339R 6.85e-1 BR.2.1
V3820 1016G>A missense_variant S G339D 6.87e-1 BR.2.1
V3840 1112C>T missense_variant S S371F 6.79e-1 BR.2.1
V3841 1117T>C missense_variant S S373P 6.78e-1 BR.2.1
V3843 1124C>T missense_variant S S375F 6.81e-1 BR.2.1
V3844 1126A>G missense_variant S T376A 6.88e-1 BR.2.1
V3851 1213G>A missense_variant S D405N 6.74e-1 BR.2.1
V3854 1224A>C missense_variant S R408S 6.69e-1 BR.2.1
V3861 1251G>T missense_variant S K417N 6.67e-1 BR.2.1
V4144 2862A>T missense_variant S Q954H 7.82e-1 BR.2.1
V4146 2907T>A missense_variant S N969K 7.85e-1 BR.2.1
V4729 55C>G missense_variant M Q19E 6.26e-1 BR.2.1
V5241 -3A>T upstream_gene_variant N None 6.43e-1 BR.2.1
V5651 1237A>C missense_variant N S413R 6.35e-1 BR.2.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.42e-1 BR.2.1
V7888 15450C>T synonymous_variant ORF1ab_pp1ab L5150L 7.57e-1 BR.2.1
V9076 3438C>T synonymous_variant S D1146D 7.73e-1 BR.2.1
V9496 52C>T synonymous_variant ORF7b L18L 6.17e-1 BR.2.1
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 8.38e-1 BR.2
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 7.20e-1 BR.2
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 7.57e-1 BR.2
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 7.70e-1 BR.2
V3784 769G>A missense_variant S G257S 6.27e-1 BR.2
V3818 1015G>C missense_variant S G339R 6.95e-1 BR.2
V3820 1016G>A missense_variant S G339D 7.26e-1 BR.2
V3824 1037G>C missense_variant S R346T 7.16e-1 BR.2
V3840 1112C>T missense_variant S S371F 6.60e-1 BR.2
V3841 1117T>C missense_variant S S373P 6.60e-1 BR.2
V3843 1124C>T missense_variant S S375F 6.68e-1 BR.2
V3844 1126A>G missense_variant S T376A 6.68e-1 BR.2
V3851 1213G>A missense_variant S D405N 6.30e-1 BR.2
V4144 2862A>T missense_variant S Q954H 7.85e-1 BR.2
V4146 2907T>A missense_variant S N969K 8.32e-1 BR.2
V5651 1237A>C missense_variant N S413R 6.16e-1 BR.2
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.18e-1 BR.2
V7888 15450C>T synonymous_variant ORF1ab_pp1ab L5150L 6.70e-1 BR.2
V8457 19791A>G synonymous_variant ORF1ab_pp1ab E6597E 6.02e-1 BR.2
V9076 3438C>T synonymous_variant S D1146D 6.58e-1 BR.2
V1554 6563C>T missense_variant ORF1ab_pp1a S2188F 1.00e+0 BU.1
V19 -166C>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 BU.1
V2462 13253C>T missense_variant ORF1ab_pp1ab T4418I 7.07e-1 BU.1
V8256 18207T>C synonymous_variant ORF1ab_pp1ab D6069D 7.07e-1 BU.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 6.42e-1 BY.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.07e-1 BY.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.31e-1 CA.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.29e-1 CA.7
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 9.33e-1 CH.1.1.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.54e-1 CH.1.1.1
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 9.07e-1 CH.1.1.2
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.12e-1 CH.1.1.2
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 9.34e-1 CH.1.1.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.74e-1 CH.1.1.3
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 8.16e-1 CH.1.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 6.49e-1 CH.1.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 8.21e-1 CJ.1
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F 6.37e-1 CJ.1
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F -7.45e-1 CJ.1
V569 1666C>A missense_variant ORF1ab_pp1a Q556K -8.11e-1 CJ.1
V6254 2689T>C synonymous_variant ORF1ab_pp1a L897L -7.62e-1 CJ.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.34e-1 CJ.1
V7437 11895G>A synonymous_variant ORF1ab_pp1a E3965E -7.45e-1 CJ.1
V1347 5557C>T missense_variant ORF1ab_pp1a L1853F 7.07e-1 CM.2
V8654 216G>A synonymous_variant S G72G 1.00e+0 P.1.14
V1243 4798G>A missense_variant ORF1ab_pp1a D1600N 6.32e-1 P.1.2
V3236 19405G>A missense_variant ORF1ab_pp1ab G6469R 7.07e-1 P.1.2
V4151 3017C>T missense_variant S T1006I 7.07e-1 P.1.2
V4152 3047C>T missense_variant S A1016V 1.00e+0 P.1.2
V8834 1623C>T synonymous_variant S F541F 7.07e-1 P.1.2
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 XBB.1.2
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 7.54e-1 XBB.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.41e-1 XBB.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.16e-1 XBB.2
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 8.63e-1 XBB.3
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 8.82e-1 XBB.3
V3784 769G>A missense_variant S G257S 7.82e-1 XBB.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.43e-1 XBB.3
V8431 19590C>T synonymous_variant ORF1ab_pp1ab D6530D 7.04e-1 XBB.3
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 9.35e-1 XBB
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 9.35e-1 XBB
V4234 3550G>T missense_variant S D1184Y 6.12e-1 XBB
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 XBB
V7113 9435C>T synonymous_variant ORF1ab_pp1a I3145I 1.00e+0 XBF
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 8.39e-1 XBK
V187 247_255delCATGTTATG conservative_inframe_deletion ORF1ab_pp1a H83_M85del -8.01e-1 XBK
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F 6.01e-1 XBK
V403 1037C>T missense_variant ORF1ab_pp1a T346I -8.01e-1 XBK
V448 1198G>A missense_variant ORF1ab_pp1a G400S -8.01e-1 XBK
V602 1771G>T missense_variant ORF1ab_pp1a A591S -8.01e-1 XBK
V6120 1830G>A synonymous_variant ORF1ab_pp1a S610S -8.01e-1 XBK
V6352 3423C>T synonymous_variant ORF1ab_pp1a H1141H -7.34e-1 XBK
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.87e-1 XBK
V8303 18550C>T synonymous_variant ORF1ab_pp1ab L6184L -7.23e-1 XBK
V1119 3961C>T missense_variant ORF1ab_pp1a P1321S 8.16e-1 AY.5.2
V6598 5283C>T synonymous_variant ORF1ab_pp1a T1761T 1.00e+0 AY.5.2
V7676 13854G>A synonymous_variant ORF1ab_pp1ab T4618T 1.00e+0 AY.5.2
V7872 15315C>T synonymous_variant ORF1ab_pp1ab N5105N 1.00e+0 AY.5.2
V9609 225C>T synonymous_variant N N75N 1.00e+0 AY.5.2
V1475 6236C>T missense_variant ORF1ab_pp1a P2079L 1.00e+0 B.1.1.354
V3009 17851C>T missense_variant ORF1ab_pp1ab H5951Y 8.15e-1 B.1.1.354
V3553 77C>T missense_variant S P26L 1.00e+0 B.1.1.354
V3797 790G>T missense_variant S A264S 1.00e+0 B.1.1.354
V5912 399C>T synonymous_variant ORF1ab_pp1a G133G 1.00e+0 B.1.1.354
V7684 13920C>T synonymous_variant ORF1ab_pp1ab T4640T 8.15e-1 B.1.1.354
V8256 18207T>C synonymous_variant ORF1ab_pp1ab D6069D 1.00e+0 B.1.1.354
V8694 447C>T synonymous_variant S N149N 1.00e+0 B.1.1.354
V1228 4750G>A missense_variant ORF1ab_pp1a V1584M 1.00e+0 B.1.1.356
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 1.00e+0 B.1.1.356
V373 914C>T missense_variant ORF1ab_pp1a P305L 1.00e+0 B.1.1.356
V4143 2848G>A missense_variant S D950N 1.00e+0 B.1.1.356
V5337 163G>T missense_variant N A55S 1.00e+0 B.1.1.356
V8468 19914C>T synonymous_variant ORF1ab_pp1ab V6638V 1.00e+0 B.1.1.356
V864 2912C>T missense_variant ORF1ab_pp1a P971L 1.00e+0 B.1.1.356
V626 1870C>T missense_variant ORF1ab_pp1a L624F 1.00e+0 B.1.177.72
V7648 13659C>T synonymous_variant ORF1ab_pp1ab D4553D 1.00e+0 B.1.177.72
V7840 15060C>T synonymous_variant ORF1ab_pp1ab N5020N 1.00e+0 B.1.177.72
V8811 1425C>T synonymous_variant S A475A 1.00e+0 B.1.177.72
V9259 819G>T synonymous_variant ORF3a V273V 9.34e-1 B.1.177.72
V5151 193G>T missense_variant ORF8 A65S 1.00e+0 B.1.575.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 7.02e-1 BA.2.10.4
V1507 6344G>T missense_variant ORF1ab_pp1a R2115I 1.00e+0 BA.2.10.4
V1604 6833T>C missense_variant ORF1ab_pp1a I2278T 1.00e+0 BA.2.10.4
V222 329A>G missense_variant ORF1ab_pp1a H110R 1.00e+0 BA.2.10.4
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 1.00e+0 BA.2.10.4
V3303 19819G>A missense_variant ORF1ab_pp1ab V6607I 1.00e+0 BA.2.10.4
V3818 1015G>C missense_variant S G339R 1.00e+0 BA.2.10.4
V3891 1380T>G missense_variant S N460K 1.00e+0 BA.2.10.4
V4324 59T>C missense_variant ORF3a I20T 1.00e+0 BA.2.10.4
V4664 31A>G missense_variant E T11A 1.00e+0 BA.2.10.4
V4856 23C>T missense_variant ORF7a A8V 1.00e+0 BA.2.10.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BA.2.10.4
V8583 20952C>T synonymous_variant ORF1ab_pp1ab H6984H 1.00e+0 BA.2.10.4
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 1.00e+0 BA.2.38.3
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 1.00e+0 BA.2.38.3
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 1.00e+0 BA.2.38.3
V5457 604A>T missense_variant N S202C 1.00e+0 BA.2.38.3
V5459 605G>C missense_variant N S202T 1.00e+0 BA.2.38.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BA.2.38.3
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 1.00e+0 BA.2.38.3
V8593 20994A>G synonymous_variant ORF1ab_pp1ab S6998S 1.00e+0 BA.2.38.3
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 1.00e+0 BA.2.38.4
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 1.00e+0 BA.2.38.4
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 1.00e+0 BA.2.38.4
V4063 2292C>A missense_variant S N764K -7.06e-1 BA.2.38.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BA.2.38.4
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 1.00e+0 BA.2.38.4
V7697 14001C>T synonymous_variant ORF1ab_pp1ab F4667F 1.00e+0 BA.2.38.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.15e-1 BA.2.75.10
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.42e-1 BA.2.75.6
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.41e-1 BA.2.75.7
V3015 17899A>G missense_variant ORF1ab_pp1ab I5967V 7.02e-1 BA.2.75.8
V3547 71T>C missense_variant S L24S -7.02e-1 BA.2.75.8
V6265 2772C>T synonymous_variant ORF1ab_pp1a F924F 7.02e-1 BA.2.75.8
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BA.2.75.8
V6379 3696C>T synonymous_variant ORF1ab_pp1a I1232I 1.00e+0 BA.2.75.8
V9334 336C>T synonymous_variant M F112F 1.00e+0 BA.2.75.8
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 1.00e+0 BH.1
V3891 1380T>G missense_variant S N460K 7.06e-1 BH.1
V3957 1721A>T missense_variant S D574V 1.00e+0 BH.1
V4664 31A>G missense_variant E T11A 1.00e+0 BH.1
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F 7.05e-1 BJ.1
V6278 2865C>T synonymous_variant ORF1ab_pp1a Y955Y 1.00e+0 BJ.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BJ.1
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 7.01e-1 BL.1.4
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 7.01e-1 BL.1.4
V1556 6578C>T missense_variant ORF1ab_pp1a S2193F -7.01e-1 BL.1.4
V2037 10184C>A missense_variant ORF1ab_pp1a P3395H 7.01e-1 BL.1.4
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 7.01e-1 BL.1.4
V4144 2862A>T missense_variant S Q954H 7.01e-1 BL.1.4
V4146 2907T>A missense_variant S N969K 7.01e-1 BL.1.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BL.1.4
V7219 10182G>A synonymous_variant ORF1ab_pp1a R3394R 7.01e-1 BL.1.4
V7888 15450C>T synonymous_variant ORF1ab_pp1ab L5150L 7.01e-1 BL.1.4
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 7.85e-1 BL.3
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 6.22e-1 BL.3
V1759 8053C>T missense_variant ORF1ab_pp1a P2685S 6.10e-1 BL.3
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 6.95e-1 BL.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.62e-1 BL.3
V8010 16383G>A synonymous_variant ORF1ab_pp1ab T5461T -6.22e-1 BL.3
V8457 19791A>G synonymous_variant ORF1ab_pp1ab E6597E 6.56e-1 BL.3
V3273 19691C>T missense_variant ORF1ab_pp1ab T6564I 6.24e-1 BL.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.25e-1 BL.4
V5997 921G>A synonymous_variant ORF1ab_pp1a A307A -6.57e-1 BL.5
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.47e-1 BL.5
V6040 1248C>T synonymous_variant ORF1ab_pp1a C416C -1.00e+0 BL.6
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.53e-1 BM.1.1.5
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.62e-1 BM.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 7.67e-1 BM.2.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.67e-1 BM.2.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 6.02e-1 BM.2
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.98e-1 BM.2
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 7.42e-1 BM.4.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 7.02e-1 BM.4.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 6.60e-1 BM.4.1
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 1.00e+0 BM.4
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 1.00e+0 BM.4
V2388 12589C>T missense_variant ORF1ab_pp1a P4197S -7.01e-1 BM.4
V391 989C>T missense_variant ORF1ab_pp1a S330L -7.01e-1 BM.4
V4596 668C>T missense_variant ORF3a T223I 1.00e+0 BM.4
V5539 794C>T missense_variant N T265I -1.00e+0 BM.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BM.4
V6426 4056C>T synonymous_variant ORF1ab_pp1a A1352A 7.01e-1 BM.4
V7888 15450C>T synonymous_variant ORF1ab_pp1ab L5150L 1.00e+0 BM.4
V5579 1006G>T missense_variant N A336S -7.06e-1 BN.1.1.1
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L -7.06e-1 BN.1.1.1
V7888 15450C>T synonymous_variant ORF1ab_pp1ab L5150L 7.06e-1 BN.1.1.1
V9564 39C>T synonymous_variant N P13P -7.06e-1 BN.1.1.1
V4886 106T>C missense_variant ORF7a S36P -7.05e-1 BN.1.3.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.65e-1 BN.1.3.3
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 1.00e+0 BN.1.3.4
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 1.00e+0 BN.1.3.4
V2773 16078T>C missense_variant ORF1ab_pp1ab S5360P -1.00e+0 BN.1.3.4
V3874 1333G>C missense_variant S V445L -7.01e-1 BN.1.3.4
V3917 1457T>C missense_variant S F486S -7.01e-1 BN.1.3.4
V5313 97A>G missense_variant N S33G -1.00e+0 BN.1.3.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BN.1.3.4
V7892 15474C>T synonymous_variant ORF1ab_pp1ab F5158F -7.01e-1 BN.1.3.4
V7918 15675T>C synonymous_variant ORF1ab_pp1ab D5225D -1.00e+0 BN.1.3.4
V8173 17595T>C synonymous_variant ORF1ab_pp1ab Y5865Y -1.00e+0 BN.1.3.4
V8265 18291C>T synonymous_variant ORF1ab_pp1ab D6097D -1.00e+0 BN.1.3.4
V8375 19062A>G synonymous_variant ORF1ab_pp1ab P6354P -7.01e-1 BN.1.3.4
V8720 663G>A synonymous_variant S S221S -1.00e+0 BN.1.3.4
V9576 90A>T synonymous_variant N G30G -7.01e-1 BN.1.3.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.10e-1 BN.1.4.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BN.1.6
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.73e-1 BN.1.8
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.00e-1 BN.2.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 6.02e-1 BN.2
V2013 10021A>G missense_variant ORF1ab_pp1a I3341V -7.89e-1 BN.3
V2855 16748C>T missense_variant ORF1ab_pp1ab S5583L -7.66e-1 BN.3
V3157 18751T>C missense_variant ORF1ab_pp1ab F6251L -7.89e-1 BN.3
V5841 48C>T synonymous_variant ORF1ab_pp1a L16L -7.89e-1 BN.3
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 8.08e-1 BN.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.08e-1 BN.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.77e-1 BN.5
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 6.57e-1 BN.6
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 6.29e-1 BR.1.2
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.86e-1 BR.1.2
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 6.60e-1 BR.3
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 8.97e-1 BR.3
V2037 10184C>A missense_variant ORF1ab_pp1a P3395H 7.33e-1 BR.3
V2457 13234A>G missense_variant ORF1ab_pp1ab T4412A 6.45e-1 BR.3
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 8.32e-1 BR.3
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 8.04e-1 BR.3
V3784 769G>A missense_variant S G257S 8.16e-1 BR.3
V3818 1015G>C missense_variant S G339R 8.04e-1 BR.3
V3820 1016G>A missense_variant S G339D 8.04e-1 BR.3
V3824 1037G>C missense_variant S R346T 7.78e-1 BR.3
V3840 1112C>T missense_variant S S371F 8.04e-1 BR.3
V3841 1117T>C missense_variant S S373P 8.04e-1 BR.3
V3843 1124C>T missense_variant S S375F 8.04e-1 BR.3
V3844 1126A>G missense_variant S T376A 8.04e-1 BR.3
V3851 1213G>A missense_variant S D405N 7.33e-1 BR.3
V3854 1224A>C missense_variant S R408S 6.04e-1 BR.3
V3861 1251G>T missense_variant S K417N 6.60e-1 BR.3
V4144 2862A>T missense_variant S Q954H 8.97e-1 BR.3
V4146 2907T>A missense_variant S N969K 8.97e-1 BR.3
V5241 -3A>T upstream_gene_variant N None 7.11e-1 BR.3
V5651 1237A>C missense_variant N S413R 6.76e-1 BR.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.69e-1 BR.3
V7219 10182G>A synonymous_variant ORF1ab_pp1a R3394R 7.33e-1 BR.3
V7888 15450C>T synonymous_variant ORF1ab_pp1ab L5150L 7.93e-1 BR.3
V8457 19791A>G synonymous_variant ORF1ab_pp1ab E6597E 6.83e-1 BR.3
V9076 3438C>T synonymous_variant S D1146D 8.04e-1 BR.3
V4019 2037T>G missense_variant S N679K 6.54e-1 BR.4
V4022 2042C>A missense_variant S P681H 6.54e-1 BR.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 BR.4
V6426 4056C>T synonymous_variant ORF1ab_pp1a A1352A 6.54e-1 BR.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.46e-1 BY.1.1.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 8.73e-1 BY.1.1
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F 6.67e-1 BY.1.1
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F -6.12e-1 BY.1.1
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 7.64e-1 BY.1.1
V2576 13993T>C missense_variant ORF1ab_pp1ab Y4665H -6.12e-1 BY.1.1
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 7.64e-1 BY.1.1
V2839 16671G>A missense_variant ORF1ab_pp1ab M5557I -6.12e-1 BY.1.1
V2860 16775A>G missense_variant ORF1ab_pp1ab N5592S -6.12e-1 BY.1.1
V4718 7G>A missense_variant M D3N 7.64e-1 BY.1.1
V569 1666C>A missense_variant ORF1ab_pp1a Q556K -6.12e-1 BY.1.1
V6057 1362C>T synonymous_variant ORF1ab_pp1a L454L 6.00e-1 BY.1.1
V6254 2689T>C synonymous_variant ORF1ab_pp1a L897L -6.12e-1 BY.1.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.73e-1 BY.1.1
V1969 9601C>T missense_variant ORF1ab_pp1a L3201F 7.04e-1 BY.1.2
V2215 11269G>T missense_variant ORF1ab_pp1a G3757C -7.04e-1 BY.1.2
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.13e-1 BY.1.2
V1422 6071C>T missense_variant ORF1ab_pp1a S2024L 6.34e-1 CA.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.56e-1 CA.1
V6546 4927C>T synonymous_variant ORF1ab_pp1a L1643L 6.04e-1 CA.1
V3273 19691C>T missense_variant ORF1ab_pp1ab T6564I 6.55e-1 CA.2
V8457 19791A>G synonymous_variant ORF1ab_pp1ab E6597E 6.55e-1 CA.2
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 7.06e-1 CA.3.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 6.29e-1 CA.3.1
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 1.00e+0 CA.4
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 1.00e+0 CA.4
V2037 10184C>A missense_variant ORF1ab_pp1a P3395H 1.00e+0 CA.4
V2163 11023_11031delTCTGGTTTT conservative_inframe_deletion ORF1ab_pp1a S3675_F3677del 6.99e-1 CA.4
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 1.00e+0 CA.4
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 1.00e+0 CA.4
V3635 425G>A missense_variant S G142D 1.00e+0 CA.4
V3652 439A>G missense_variant S K147E 1.00e+0 CA.4
V3662 454T>C missense_variant S W152R 1.00e+0 CA.4
V3675 471C>A missense_variant S F157L 1.00e+0 CA.4
V3724 628A>G missense_variant S I210V 1.00e+0 CA.4
V3735 638T>G missense_variant S V213G 1.00e+0 CA.4
V3784 769G>A missense_variant S G257S 1.00e+0 CA.4
V3818 1015G>C missense_variant S G339R 1.00e+0 CA.4
V3820 1016G>A missense_variant S G339D 1.00e+0 CA.4
V3824 1037G>C missense_variant S R346T 1.00e+0 CA.4
V3840 1112C>T missense_variant S S371F 1.00e+0 CA.4
V3841 1117T>C missense_variant S S373P 1.00e+0 CA.4
V3843 1124C>T missense_variant S S375F 1.00e+0 CA.4
V3844 1126A>G missense_variant S T376A 1.00e+0 CA.4
V3851 1213G>A missense_variant S D405N 1.00e+0 CA.4
V3854 1224A>C missense_variant S R408S 1.00e+0 CA.4
V3861 1251G>T missense_variant S K417N 1.00e+0 CA.4
V4144 2862A>T missense_variant S Q954H 1.00e+0 CA.4
V4146 2907T>A missense_variant S N969K 1.00e+0 CA.4
V4242 3595G>A missense_variant S D1199N 1.00e+0 CA.4
V4729 55C>G missense_variant M Q19E 1.00e+0 CA.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 CA.4
V6426 4056C>T synonymous_variant ORF1ab_pp1a A1352A 6.99e-1 CA.4
V6546 4927C>T synonymous_variant ORF1ab_pp1a L1643L 1.00e+0 CA.4
V7193 9933C>T synonymous_variant ORF1ab_pp1a D3311D 1.00e+0 CA.4
V7219 10182G>A synonymous_variant ORF1ab_pp1a R3394R 1.00e+0 CA.4
V7888 15450C>T synonymous_variant ORF1ab_pp1ab L5150L 1.00e+0 CA.4
V8457 19791A>G synonymous_variant ORF1ab_pp1ab E6597E 1.00e+0 CA.4
V9076 3438C>T synonymous_variant S D1146D 1.00e+0 CA.4
V9135 3816C>T synonymous_variant S Y1272Y 6.99e-1 CA.4
V9139 24C>T synonymous_variant ORF3a F8F 1.00e+0 CA.4
V9496 52C>T synonymous_variant ORF7b L18L 1.00e+0 CA.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.01e-1 CA.5
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 8.24e-1 CB.1
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 7.61e-1 CB.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 9.43e-1 CB.1
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 7.66e-1 CH.1.1.4
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.49e-1 CH.1.1.4
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 6.65e-1 CH.1.1.5
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 6.65e-1 CH.1.1.5
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 1.00e+0 CH.3.1
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 9.57e-1 CH.3.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 9.57e-1 CH.3.1
V2037 10184C>A missense_variant ORF1ab_pp1a P3395H 9.57e-1 CH.3.1
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 9.57e-1 CH.3.1
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 8.47e-1 CH.3.1
V3534 56C>T missense_variant S T19I 7.79e-1 CH.3.1
V3544 71_79delTACCCCCTG disruptive_inframe_deletion S L24_A27delinsS 8.28e-1 CH.3.1
V3635 425G>A missense_variant S G142D 8.71e-1 CH.3.1
V3652 439A>G missense_variant S K147E 9.14e-1 CH.3.1
V3662 454T>C missense_variant S W152R 9.14e-1 CH.3.1
V3675 471C>A missense_variant S F157L 9.57e-1 CH.3.1
V3724 628A>G missense_variant S I210V 1.00e+0 CH.3.1
V3735 638T>G missense_variant S V213G 1.00e+0 CH.3.1
V3784 769G>A missense_variant S G257S 1.00e+0 CH.3.1
V3818 1015G>C missense_variant S G339R 9.57e-1 CH.3.1
V3820 1016G>A missense_variant S G339D 9.57e-1 CH.3.1
V3824 1037G>C missense_variant S R346T 9.57e-1 CH.3.1
V3840 1112C>T missense_variant S S371F 9.57e-1 CH.3.1
V3841 1117T>C missense_variant S S373P 9.57e-1 CH.3.1
V3843 1124C>T missense_variant S S375F 9.57e-1 CH.3.1
V3844 1126A>G missense_variant S T376A 9.57e-1 CH.3.1
V3851 1213G>A missense_variant S D405N 1.00e+0 CH.3.1
V3854 1224A>C missense_variant S R408S 1.00e+0 CH.3.1
V3861 1251G>T missense_variant S K417N 1.00e+0 CH.3.1
V3868 1320T>G missense_variant S N440K 6.45e-1 CH.3.1
V4144 2862A>T missense_variant S Q954H 1.00e+0 CH.3.1
V4146 2907T>A missense_variant S N969K 1.00e+0 CH.3.1
V4729 55C>G missense_variant M Q19E 7.63e-1 CH.3.1
V5241 -3A>T upstream_gene_variant N None 7.63e-1 CH.3.1
V5305 90_98delAGAACGCAG disruptive_inframe_deletion N E31_S33del 6.17e-1 CH.3.1
V5651 1237A>C missense_variant N S413R 9.57e-1 CH.3.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 CH.3.1
V7193 9933C>T synonymous_variant ORF1ab_pp1a D3311D 1.00e+0 CH.3.1
V7219 10182G>A synonymous_variant ORF1ab_pp1a R3394R 9.57e-1 CH.3.1
V7888 15450C>T synonymous_variant ORF1ab_pp1ab L5150L 9.18e-1 CH.3.1
V8457 19791A>G synonymous_variant ORF1ab_pp1ab E6597E 8.71e-1 CH.3.1
V9076 3438C>T synonymous_variant S D1146D 9.57e-1 CH.3.1
V9496 52C>T synonymous_variant ORF7b L18L 7.24e-1 CH.3.1
V97 -25C>T upstream_gene_variant ORF1ab_pp1a None 8.28e-1 CH.3.1
V1040 3592C>A missense_variant ORF1ab_pp1a Q1198K 1.00e+0 CH.3
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 6.97e-1 CH.3
V3091 18319G>A missense_variant ORF1ab_pp1ab V6107I 1.00e+0 CH.3
V3724 628A>G missense_variant S I210V 1.00e+0 CH.3
V3784 769G>A missense_variant S G257S 6.97e-1 CH.3
V3868 1320T>G missense_variant S N440K 6.97e-1 CH.3
V3877 1336G>A missense_variant S G446S 6.97e-1 CH.3
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 CH.3
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 6.97e-1 CH.3
V9334 336C>T synonymous_variant M F112F 6.97e-1 CH.3
V9401 58A>C synonymous_variant ORF6 R20R 1.00e+0 CH.3
V112 -5G>A upstream_gene_variant ORF1ab_pp1a None 6.60e-1 CJ.1.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 8.19e-1 CJ.1.1
V2326 12179A>G missense_variant ORF1ab_pp1a N4060S 8.75e-1 CJ.1.1
V3091 18319G>A missense_variant ORF1ab_pp1ab V6107I 9.17e-1 CJ.1.1
V3652 439A>G missense_variant S K147E 7.18e-1 CJ.1.1
V3662 454T>C missense_variant S W152R 7.44e-1 CJ.1.1
V3675 471C>A missense_variant S F157L 8.04e-1 CJ.1.1
V3724 628A>G missense_variant S I210V 8.19e-1 CJ.1.1
V3784 769G>A missense_variant S G257S 8.49e-1 CJ.1.1
V3874 1333G>C missense_variant S V445L -9.17e-1 CJ.1.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 CJ.1.1
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 6.72e-1 CJ.1.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.84e-1 CV.1
V2431 13064C>T missense_variant ORF1ab_pp1a T4355I -7.03e-1 CV.2
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 7.03e-1 CV.2
V4107 2567A>G missense_variant S N856S -7.03e-1 CV.2
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 CV.2
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 1.00e+0 XBC.1
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 1.00e+0 XBC.1
V1608 6854C>T missense_variant ORF1ab_pp1a S2285F 7.06e-1 XBC.1
V1929 9226C>T missense_variant ORF1ab_pp1a H3076Y 7.06e-1 XBC.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 XBC.1
V6426 4056C>T synonymous_variant ORF1ab_pp1a A1352A 1.00e+0 XBC.1
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 1.00e+0 XBC.1
V7011 8586G>T synonymous_variant ORF1ab_pp1a V2862V 1.00e+0 XBC.1
V9368 480C>T synonymous_variant M D160D 7.06e-1 XBC.1
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 8.91e-1 XBD
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 7.03e-1 XBH
V1863 8672C>T missense_variant ORF1ab_pp1a A2891V 1.00e+0 XBH
V194 252_254delTAT disruptive_inframe_deletion ORF1ab_pp1a M85del 1.00e+0 XBH
V1989 9851C>T missense_variant ORF1ab_pp1a T3284I 1.00e+0 XBH
V3273 19691C>T missense_variant ORF1ab_pp1ab T6564I -7.03e-1 XBH
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 1.00e+0 XBH
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 1.00e+0 XBH
V6546 4927C>T synonymous_variant ORF1ab_pp1a L1643L 1.00e+0 XBH
V6651 5721C>T synonymous_variant ORF1ab_pp1a F1907F 1.00e+0 XBH
V7587 13113C>T synonymous_variant ORF1ab_pp1a T4371T 1.00e+0 XBH
V912 3065C>T missense_variant ORF1ab_pp1a T1022I 1.00e+0 XBH
V9598 159C>T synonymous_variant N F53F 7.03e-1 XBH
V1114 3919G>A missense_variant ORF1ab_pp1a G1307S 7.03e-1 XBL
V2037 10184C>A missense_variant ORF1ab_pp1a P3395H 7.03e-1 XBL
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 7.03e-1 XBL
V3702 547C>G missense_variant S Q183E 7.03e-1 XBL
V3733 638T>A missense_variant S V213E 7.03e-1 XBL
V6364 3531C>T synonymous_variant ORF1ab_pp1a V1177V 7.03e-1 XBL
V7219 10182G>A synonymous_variant ORF1ab_pp1a R3394R 7.03e-1 XBL
V8457 19791A>G synonymous_variant ORF1ab_pp1ab E6597E 7.03e-1 XBL
V9139 24C>T synonymous_variant ORF3a F8F 7.03e-1 XBL
V937 3181G>A missense_variant ORF1ab_pp1a A1061T 7.03e-1 XBL





Manual curation of mutation (3662C>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