Table 1.
Number of Variants per Sample
| S23 Mutant | S23 Repaired | All Variants | Filtered Variants | Filtered SNV | Filtered Del | Filtered Insert |
|---|---|---|---|---|---|---|
| 0/0 | 0/1 | 66,758 | 46,002 | 36,147 | 4,681 | 5,174 |
| 0/1 | 0/0 | 67,563 | 46,414 | 36,637 | 4,684 | 5,093 |
| 0/0 | 1/1 | 8,579 | 644 | 105 | 307 | 232 |
| 1/1 | 0/0 | 8,414 | 729 | 92 | 345 | 292 |
| 0/1 | 1/1 | 23,814 | 6,322 | 4,490 | 890 | 942 |
| 1/1 | 0/1 | 22,472 | 5,675 | 4,046 | 769 | 860 |
| 0/1 | 0/1 | 1,074,296 | 971,609 | 798,079 | 92,812 | 80,718 |
| 1/1 | 1/1 | 1,036,972 | 549,872 | 441,444 | 35,296 | 73,132 |
| Total | 2,308,868 | 1,627,267 | 1,321,040 | 139,784 | 166,443 | |
The genotype conventions were followed: “0/0” refers to homozygous reference position (no variant), “0/1” heterozygous, and “1/1” homozygous alternative. “Filtered” refers to the minimum coverage of 10 in both samples and a minimum of three for the alternative alleles, which reduces the number of variants by 30% but ensures that both samples have a good coverage. We can observe that the new variants in sample S23 repaired (0/0 0/1 or 0/0 1/1) and the new variants in sample S23 mutant (0/1 0/0 or 1/1 0/0) are very similar. Thus, we cannot see a big increase or decrease in the overall number of variants between these two samples. SNV, single nucleotide variant; Del, deletions; Insert, insertions.