Identifying featured indels associated with SARS-CoV-2 fitness

  

Figure S1: The number of indel types in genes and intergenic regions. 

Figure S2: The point indicates the concrete position and number of each deletion type. Color indicated the gene to which each deletion type belongs. 

Figure S3: The point indicates the concrete position and number of each insertion type. Color indicated the gene to which each insertion type belongs. 

Figure S4: Heatmap of 626 Pango lineages and 65 indel types. The color indicates the ratio of sequences contained indels in corresponding Pango lineage.

Figure S5: These figures show change of the number of sequences contained corresponding indels with time and change of the number of sequences in different variants.

Figure S6: The upset diagram exhibits all combinations of 4 featured deletions and corresponding number. The color in each combination means the Pango lineages of Alpha variant.

Figure S7: The upset diagram exhibits all combinations of 3 featured deletions and corresponding number. The color in each combination means the Pango lineages of Delta variant.

Figure S8: The upset diagram exhibits all combinations of 6 featured deletions and 1 featured insertion, and corresponding number. The color in each combination means the Pango lineages belonging to BA.1 and descendent lineages of Omicron variant.

Figure S9: The upset diagram exhibits all combinations of 3 featured deletions and corresponding number. The color in each combination means the Pango lineages belonging to BA.2 and descendent lineages of Omicron variant.

Figure S10: The upset diagram exhibits all combinations of 5 featured deletions and corresponding number. The color in each combination means the Pango lineages belonging to BA.3 and descendent lineages of Omicron variant.

Figure S11: The upset diagram exhibits all combinations of 5 featured deletions and corresponding number. The color in each combination means the Pango lineages belonging to BA.4 and descendent lineages of Omicron variant.

Figure S12: The upset diagram exhibits all combinations of 4 featured deletions and corresponding number. The color in each combination means the Pango lineages belonging to BA.5 and descendent lineages of Omicron variant. 

Figure S13: The upset diagram exhibits all combinations of 2 featured deletions and corresponding number. The color in each combination means the Pango lineages of Beta variant. 

Figure S14: The upset diagram exhibits all combinations of 2 featured deletions and corresponding number. The color in each combination means the Pango lineages of Gamma variant. 

Figure S15: The upset diagram exhibits all combinations of 2 featured deletions and corresponding number. The color in each combination means the Pango lineages of Mu variant. 

Figure S16: The upset diagram exhibits all combinations of 2 featured deletions and corresponding number. The color in each combination means the Pango lineages of Iota variant. 

Figure S17: The upset diagram exhibits all combinations of 5 featured deletions and corresponding number. The color in each combination means the Pango lineages of Eta variant. 

Figure S18: The figure exhibits the growth rates of all Pango lineages estimated with only substitution mutations. Color indicates the variants. Size of circle indicates the number of sequences of a Pango lineage.

Figure S19: The figure exhibits the selection coefficient of different mutations. Red points indicate selection coefficient of top 10 substitutions. Beta represents the selection coefficient.

  

Table S1: Details of 26,765 types of deletions and 21,054 types of insertions. The start means the start site where deletion/insertion occurred. Length means the length of deleted/inserted sequences. Sequence of insertion means the concrete inserted nucleotides. Count means number of indel records of each indel type. 

Table S2: The distribution about length of all indel records. Freq means the number of indels records with the same length regardless of whether they are of the same indel type. 

Table S3: The table indicates the number of all sequences with a specific number of deletions and insertions. 

Table S4: The table indicates the number of indel types with frameshift or non-frameshift in different genes. All indel types were counted. 

Table S5: This table indicates the ratio of 47,819 indel types and 1,446 Pango lineages. Only Pango lineages have indels will be presented here. 

Table S6: This table indicates the ratio of 65 indel types and 626 Pango lineages. Each Pango lineages here have at least one indel type which occurred in more than 80% of all sequences of this lineage.

Table S7: The table shows the number of sequences of 7 combinations in Alpha variant on 6 continents. 

Table S8: The table shows the number of sequences 7 combinations in Delta variant on 6 continents. 

Table S9: The table shows the number of 9 combinations of BA.1 and descendent lineages belonging to Omicron variant on 6 continents. 

Table S10: The table shows refined clades. clade0 indicates the original clade refined only with substitution mutations. Clade0 was divided into clade1 and clade2 based on indels. Count0, count1 and count2 correspond to clade0, clade1 and clade2, and the same for lineage0, lineage1 and lineage2. Diff_mut1 and diff_mut2 indicate unique mutations in clade1 and clade2. Fitness0, fitness1 and fitness2 correspond to fitness of clade0, clade1 and clade2. All_mut1 and all_mut2 corresponds to all mutations belonging to clade1 and clade2.

Table S11: The table shows the growth rates estimated with substitution and indel mutations of Pango lineages.

Table S12: The table shows the growth rates estimated with only substitution mutations of Pango lineages.

Table S13: The table shows the selection coefficients of substitution and indel mutations.

Table S14: The table shows the selection coefficients of substitution mutations.

Table S15: The table shows the precision and sensitivity of simulation in 1,000 times.