Table 1.
Somatic SNVs Identified Using MuTect2 with Allele Frequency ≥ 0.25 and Read Depth ≥ 10
| Chromosome | Position | Reference | Altered | AD | AF | Gene | Type | SNVs | Change |
|---|---|---|---|---|---|---|---|---|---|
| Sample 1: hESC SKO-B2M | |||||||||
| chr3 | 194077829 | G | A | 16; 14 | 0.467 | LRRC15 | 3ʹ UTR | SNP | |
| chr11 | 64820793 | A | G | 15; 8 | 0.348 | NAALADL1 | Silent | SNP | |
| chr13 | 45969047 | CTT | C | 10; 18 | 0.63 | SLC25A30 | 3ʹ UTR | DEL | |
| chr15 | 22945136 | C | T | 18; 9 | 0.346 | CYFIP1 | Nonsense_Mutation | SNP | ENSP00000324549:p.Gln403∗ |
| chr15 | 45003753 | C | CT | 0; 24 | 1 | B2M | Frame_Shift_Ins | INS | ENSP00000452780:p.Ser4fs |
| Sample 2: hESC DKO | |||||||||
| chr16 | 10989283 | CA | C | 0; 12 | 1 | CIITA | Frame_Shift_Del | DEL | ENSP00000316328:p.Ser66fs |
Total non-redundant exonic regions considered in the analysis: 229,235 (26,201 unique genes).
AD, allelic depths for the reference and altered alleles in the order listed; AF, allele fraction of the event in the hESC WT and hESC SKO-B2M (sample 1); or hESC SKO-B2M and hESC DKO (sample 2).