TABLE 3.
Numbers of different types of InDels in each sample.
| Category |
Sample |
|||
| 132000B-3 | 827-3 | Pool-1 | Pool-2 | |
| Upstream | 88,355 | 82,198 | 85,618 | 86,359 |
| Exonic | ||||
| Stop gain | 311 | 267 | 302 | 304 |
| Stop loss | 91 | 84 | 84 | 85 |
| Frameshift deletion | 3690 | 3603 | 3654 | 3685 |
| Frameshift insertion | 3269 | 3123 | 3191 | 3214 |
| Non-frameshift deletion | 5712 | 5205 | 5528 | 5553 |
| Non-frameshift insertion | 5176 | 4569 | 4938 | 4976 |
| Intronic | 106,908 | 96,371 | 101,716 | 102,817 |
| Splicing | 1703 | 1622 | 1633 | 1648 |
| Downstream | 67,226 | 62,430 | 65,535 | 66,030 |
| Upstream/downstream | 20,893 | 19,013 | 19,687 | 19,947 |
| Intergenic | 237,048 | 228,308 | 241,855 | 242,736 |
| Insertion | 257,432 | 240,462 | 254,288 | 256,036 |
| Deletion | 284,237 | 267,619 | 280,737 | 282,605 |
| Total | 541,669 | 508,081 | 535,025 | 538,641 |
132000B-3, aberrant parental plant 132000B-3 displaying ectopic blade-like outgrowths on the adaxial side of leaf; 827-3, parental plant with normal leaves; Pool-1, bulked DNA pool for individuals with normal leaves from the F2:3 family; Pool-2, bulked DNA pool for individuals with ectopic blade-like outgrowths from the F2:3 family. Upstream, variant overlaps the 1-kb region upstream of the transcription start site; Exonic, variant overlaps a coding exon; Stop gain, an insertion/deletion that leads to the immediate creation of stop codon at the variant site; Stop loss, an insertion/deletion that leads to the immediate elimination of a stop codon at the variant site; Frameshift deletion, a deletion causing a frameshift; Frameshift insertion, an insertion leading to a frameshift; Non-frameshift deletion, a deletion causing no frameshift; Non-frameshift insertion, an insertion leading to no frameshift; Intronic, variant overlaps an intron; Splicing, variant is within 2 bp of a splicing junction (use -splicing_threshold to change this); Downstream, variant overlaps the 1-kb region downstream of transcription end site (use -neargene to change this); Upstream/downstream, variant overlaps the 1-kb region upstream of transcription start site for a gene, while it overlaps 1-kb region downstream of transcription end site of another gene at the same time; Intergenic, variant is in the intergenic region.