Table 4 Line-specific SNPs not reported in dbSNP
From: SNP-based analysis of genetic diversity in anther-derived rice by whole genome sequencing
| Â | Region/type | Hwayeong | BLB | HY-04 | HY-08 | ||||
|---|---|---|---|---|---|---|---|---|---|
(#) | (%) | (#) | (%) | (#) | (%) | (#) | (%) | ||
Location | Total lsSNP | 2,599 | 2,160 | 9,602 | 5,685 | ||||
Intergenic | 2,300 | (88.5) | 1,821 | (84.3) | 7,972 | (83.0) | 4,990 | (87.8) | |
Intron | 175 | (6.7) | 172 | (8.0) | 887 | (9.2) | 433 | (7.6) | |
5′ UTR | 26 | (1.0) | 31 | (1.4) | 139 | (1.4) | 68 | (1.2) | |
CDS | 48 | (1.8) | 73 | (3.4) | 346 | (3.6) | 96 | (1.7) | |
Non-synonymous | 26 | (1.0) | 44 | (2.0) | 214 | (2.2) | 63 | (1.1) | |
Synonymous | 22 | (0.8) | 29 | (1.3) | 132 | (1.4) | 33 | (0.6) | |
3′ UTR | 43 | (1.7) | 49 | (2.3) | 229 | (2.4) | 85 | (1.5) | |
Exon | 7 | (0.3) | 14 | (0.6) | 29 | (0.3) | 13 | (0.2) | |
Type | Deletion | 209 | (8.0) | 267 | (12.4) | 736 | (7.7) | 590 | (10.4) |
Insertion | 288 | (11.1) | 189 | (8.8) | 1,111 | (11.5) | 840 | (14.8) | |
| Â | Substitution | 2,102 | (80.9) | 1,704 | (78.8) | 7,754 | (80.8) | 4,255 | (74.8) |