Table 1.
High confidence minor variants in F Mixed population (* indicates variants highlighted in Figure 5)
| Gene | Nucleotide Change | Variant Type | AA Change | Allele frequency (Percent) |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P0 | P1 | P2 | P3 | P4 | P5 | P6 | P7 | P8 | P9 | P10 | L2 ^ P10 | L3 ^ P10 | ||||
| UL7 | C to T | Synonymous | Phe209Phe | 9.4 | 14.0 | 23.9 | 21.8 | 23.4 | 25.7 | 22.3 | ||||||
| Between UL8/9 | G to C | Non-Coding | 7.2 | 6.4 | 8.1 | 5.9 | 9.2 | 10.6 | ||||||||
| Between UL8/9 | G Deletion (Homopolymer) | Non-Coding | 14.3 | 13.4 | 12.9 | 17.0 | 13.8 | 6.5 | 12.8 | 11.1 | ||||||
| UL9* | G to A | Missense | Arg813His | 2.0 | 3.7 | 5.7 | 14.8 | 35.1 | 43.6 | 40.1 | 10.1 | 10.9 | ||||
| UL9* | A to G | Missense | His813Arg | 49.3 | 47.8 | 46.0 | ||||||||||
| UL9 | C to T | Missense | Arg203Cys | 6.9 | 7.9 | 6.8 | 7.2 | 6.1 | 6.2 | 8.4 | 25.9 | 17.5 | ||||
| UL9 | G to A | Missense | Arg200His | 2.2 | 3.6 | 3.6 | 7.2 | 6.0 | 6.4 | 8.4 | 8.7 | 9.2 | 22.3 | 13.0 | ||
| UL9 | G to A | Missense | Ser105Asn | 2.6 | 2.4 | 2.2 | 3.1 | 5.1 | 4.1 | 3.6 | 10.2 | |||||
| UL9 | A to G | Missense | Ser105Gly | 2.3 | 3.8 | 5.6 | 5.4 | 8.0 | 10.3 | 12.5 | 15.0 | 14.4 | 14.7 | |||
| Between UL10/11 | C Insertion (Homopolymer) | Non-Coding | 4.3 | 4.1 | 3.6 | 2.1 | 3.8 | 3.6 | 3.8 | 4.7 | 5.0 | 3.6 | 3.7 | 7.4 | 6.0 | |
| UL12 | C to T | Synonymous | Leu287Leu | 11.2 | 16.4 | 22.9 | 20.1 | 28.5 | 23.8 | 23.9 | ||||||
| UL12 | C to T | Missense | Ala204Val | 7.3 | 9.2 | 11.3 | 16.8 | 17.1 | 18.9 | 3.3 | ||||||
| UL13 | C to T | Missense | Arg432Cys | 12.5 | 17.7 | 24.4 | 26.7 | 17.9 | 21.8 | 23.0 | 15.6 | 12.4 | 13.6 | 26.4 | 28.9 | |
| UL13* | G to A | Premature Stop | Trp30Stop | 2.2 | 9.9 | 16.3 | 22.4 | 23.3 | 24.7 | 26.5 | 24.0 | |||||
| UL13* | G Insertion (Homopolymer) | Premature Stop | Frameshift 118, Stop 161 | 45.0 | ||||||||||||
| UL13* | G Deletion (Homopolymer) | Premature Stop | Frameshift 118, Stop 161 | 47.5 | 35.0 | 27.8 | 19.0 | 10.3 | 10.0 | 6.2 | 6.0 | 3.3 | 2.3 | 4.7 | 3.2 | |
| UL14 | C to A | Missense | Leu135Met | 2.5 | 2.3 | 3.9 | 4.0 | 3.4 | 3.8 | 3.9 | 3.4 | 2.6 | 3.6 | 3.1 | 3.3 | |
| UL14 | C to T | Synonymous | Asp132Asp | 2.0 | 2.2 | 5.4 | 6.2 | 8.5 | 6.8 | 9.4 | 11.9 | 14.4 | 13.6 | 18.2 | 25.6 | |
| UL14* | G to A | Missense | Val109Met | 13.5 | 19.9 | 23.7 | 25.7 | 33.3 | 38.1 | 32.5 | 40.5 | 38.3 | 38.8 | 41.8 | 41.3 | 38.1 |
| UL14* | G to A | Missense | Val81Met | 2.5 | 2.6 | 2.7 | 4.8 | 6.0 | 4.1 | |||||||
| UL16* | C to T | Missense | Leu261Phe | 8.2 | 14.4 | 12.0 | 14.2 | 16.1 | 16.4 | |||||||
| UL17 | C to A | Missense | Ala227Glu | 2.1 | 2.0 | 3.4 | 3.7 | 4.3 | 4.2 | 2.7 | ||||||
| UL17 | G to A | Missense | Ala3Thr | 9.9 | 15.0 | 24.6 | 24.5 | 26.7 | 24.8 | 23.2 | ||||||
| Between UL17/18 | C Insertion (Homopolymer) | Non-Coding | 3.1 | 5.8 | 5.0 | 5.4 | 4.5 | 6.9 | 4.9 | 4.7 | ||||||
| UL18 | C to T | Synonymous | Leu275Leu | 2.4 | 3.3 | 3.1 | 2.5 | 3.1 | 3.4 | 10.6 | 12.0 | |||||
| UL19 | C to T | Missense | Pro486Leu | 2.5 | 2.5 | 3.0 | 3.7 | 3.0 | 3.5 | 4.2 | ||||||
| Between UL20/21 | C to T | Non-Coding | 3.6 | 3.3 | 2.2 | 2.6 | 2.9 | 2.2 | 2.3 | 3.1 | 2.7 | |||||
| Between UL22/23 | C to G | Non-Coding | 10.4 | 20.7 | 23.7 | 20.4 | 26.4 | 28.5 | 29.7 | |||||||
| UL22 | C to T | Synonymous | Leu480Leu | 2.5 | 2.9 | 3.5 | 3.4 | 4.4 | 4.1 | 4.6 | 3.1 | 13.3 | 14.5 | |||
| UL24 | C to T | Missense | Arg63Cys | 2.8 | 3.6 | 2.5 | 2.8 | 2.3 | 2.7 | |||||||
| UL24* | G to A | Missense | Arg265Gln | 8.1 | 12.8 | 18.9 | 18.8 | 25.1 | 22.9 | 22.4 | ||||||
| UL25 | G to A | Synonymous | Pro146Pro | 5.5 | 12.6 | 13.4 | 12.0 | 14.1 | 15.4 | |||||||
| UL25 | G to A | Missense | Ala357Thr | 3.0 | 2.9 | 4.3 | 3.5 | 2.7 | 2.1 | |||||||
| Between UL25/26 | T Insertion | Non-Coding | 16.0 | 15.3 | 12.5 | 15.5 | 18.9 | 19.8 | 26.2 | 26.6 | 23.2 | 27.2 | 25.7 | 14.5 | 16.8 | |
| UL26 | G to A | Synonymous | Ala263Ala | 6.3 | 10.1 | 13.6 | 15.3 | 15.8 | 18.4 | 4.2 | ||||||
| UL26 | C to A | Synonymous | Ala362Ala | 3.2 | 2.7 | 3.5 | 4.0 | 3.8 | 4.4 | 2.8 | ||||||
| Between UL26/27 | T Insertion | Non-Coding | 4.8 | 3.4 | 3.4 | 4.2 | 3.5 | 5.8 | 4.4 | 5.5 | 19.5 | 7.1 | ||||
| Between UL26/27 | C to T | Non-Coding | 2.5 | 12.7 | 20.4 | 30.4 | 26.3 | 35.3 | 32.9 | 28.5 | 4.9 | 5.7 | ||||
| UL27 | G to A | Missense | Arg885His | 2.9 | 3.5 | 4.1 | 5.4 | 4.8 | 4.3 | 5.2 | 8.5 | 4.7 | ||||
| UL27* | G to A | Missense | Arg858His | 3.5 | 5.8 | 12.4 | 26.2 | 31.0 | 46.3 | 49.0 | 48.6 | 35.9 | ||||
| UL27* | A to G | Missense | His858Arg | 50.1 | 48.9 | 47.3 | ||||||||||
| UL27* | T to C | Missense | Leu817Pro | 2.8 | 6.9 | 14.7 | 17.2 | 21.1 | 32.8 | 36.1 | 40.1 | 41.0 | 46.3 | 30.9 | 47.6 | |
| UL27 | G to A | Synonymous | Lys544Lys | 7.9 | 10.5 | 13.4 | 17.7 | 15.9 | 16.0 | |||||||
| UL30 | C to T | Missense | Ala25Val | 2.8 | 3.3 | 2.9 | 2.9 | 2.5 | 4.6 | 13.5 | 14.5 | |||||
| UL30 | G to A | Synonymous | Lys938Lys | 8.6 | 15.3 | 20.8 | 20.2 | 20.7 | 21.8 | 23.6 | ||||||
| UL30 | G to A | Missense | Arg181His | 2.2 | 2.9 | 3.2 | 2.1 | 3.3 | 2.4 | |||||||
| UL34 | C to T | Synonymous | Gly109Gly | 6.1 | 8.8 | 10.5 | 12.7 | 14.9 | 13.4 | |||||||
| UL36 | G to A | Missense | Ala981Thr | 2.5 | 2.2 | 3.0 | 2.6 | 2.8 | 11.4 | 7.8 | ||||||
| UL36 | C to T | Missense | Thr860Met | 3.2 | 2.6 | 3.4 | 2.3 | 2.5 | ||||||||
| UL37 | C to T | Missense | Ser890Leu | 2.6 | 2.2 | 3.2 | 3.5 | 2.4 | 3.2 | |||||||
| UL39 | G to A | Synonymous | Gln736Gln | 3.1 | 3.2 | 3.7 | 2.8 | 2.8 | ||||||||
| UL40 | C to T | Synonymous | Leu301Leu | 3.9 | 2.7 | 3.0 | 2.5 | 3.4 | 2.3 | 2.2 | ||||||
| UL42 | C to T | Missense | Thr135Met | 2.8 | 3.5 | 2.6 | 2.6 | |||||||||
| UL42 | C to T | Synonymous | Leu325Leu | 10.2 | 12.5 | 23.3 | 23.2 | 22.2 | 21.0 | 21.8 | ||||||
| UL46 | G to A | Missense | Ala185Thr | 2.0 | 2.4 | 3.7 | 2.1 | 2.2 | 2.9 | |||||||
| Between UL49/50 | G to A | Non-Coding | 2.1 | 3.2 | 2.6 | 2.2 | 2.7 | |||||||||
| Between UL53/54 | G to A | Non-Coding | 2.9 | 3.4 | 3.6 | 3.6 | 3.2 | |||||||||
| UL52 | G to A | Synonymous | Gly2Gly | 2.1 | 2.7 | 2.9 | 2.5 | |||||||||
| Between UL56/IRL | C to T | Non-Coding | 9.5 | 14.2 | 24.0 | 23.4 | 21.1 | 18.4 | ||||||||
| US6 | G to A | Synonymous | Gln52Gln | 2.0 | 2.0 | 3.3 | 3.0 | |||||||||
| US6 | C to T | Synonymous | Val356Val | 2.7 | 2.7 | 2.4 | ||||||||||
| US8A | A to G | Missense | Thr109Ala | 2.4 | 2.5 | 2.4 | 2.7 | 2.1 | ||||||||
| US8A | C to T | Missense | Ala149Val | 2.6 | 2.4 | 2.9 | 2.5 | 2.2 | 2.3 | 3.1 | 2.6 | 3.8 | 5.0 | |||
| US9 | G to A | Missense | Val65Ile | 11.4 | 12.4 | 8.7 | 11.8 | |||||||||
*
indicates variants highlighted in Figure 5. See Supplementary Files 1 (Mixed) and 2 (Purified) for full lists of Minor Variants in all passages of Lineage 1.
^
Minor variants also detected via deep-sequencing of Passage 10 (P10) of Lineages 2 or 3 (L2/L3) are listed as well.