Table 3.
Statistics of SNPs called from one resequencing and seven transcriptome data sets
| Accession name | Total # of SNP | SNP classified type
|
|||||||
|---|---|---|---|---|---|---|---|---|---|
| Homo-type | Hetero-type | ||||||||
|
|
|
||||||||
| Total # of SNP | aIntergenic region |
bGenic region
|
Total # of SNP | aIntergenic region |
bGenic region
|
||||
| cExon | Intron | cExon | Intron | ||||||
| Genome | |||||||||
| S. pimpinellifolium | 4,680,647 | 4,210,454 (89.9%) | 3,853,232 (91.5%) | 108,637 (2.6%) | 248,585 (5.9%) | 470,193 (10.1%) | 432,796 (92.0%) | 17,491 (3.8%) | 19,906 (4.2%) |
| Transcriptome | |||||||||
| PI212816 | 71,637 | 66,410 (92.7%) | 14,568 (21.9%) | 49,987 (73.8%) | 2,855 (4.3%) | 5,227 (7.3%) | 1,129 (28.2%) | 4,008 (76.7%) | 90 (1.7%) |
| PI114490 | 23,902 | 17,868 (74.8%) | 4,211 (23.6%) | 12,877 (72.1%) | 780 (4.4%) | 6,034 (25.2%) | 1,344 (22.3%) | 4,557 (75.5%) | 133 (2.2%) |
| T5 | 9,544 | 4,780 (50.1%) | 1,210 (25.3%) | 3,339 (69.9%) | 231 (4.8%) | 4,764 (49.9%) | 1,090 (22.9%) | 3,593 (75.4%) | 81 (1.7%) |
| OH9242 | 8,313 | 5,712 (68.7%) | 1,222 (21.4%) | 4,254 (74.5%) | 236 (4.1%) | 2,601 (31.3%) | 552 (21.2%) | 1,989 (76.5%) | 60 (2.3%) |
| NC84173 | 7,744 | 5,203 (67.2%) | 1,218 (23.4%) | 3,766 (72.4%) | 219 (4.2%) | 2,541 (32.8%) | 508 (20.0%) | 1,977 (77.8%) | 56 (2.2%) |
| FL7600 | 10,466 | 6,501 (62.1%) | 1,665 (25.6%) | 4,537 (69.8%) | 299 (4.6%) | 3,965 (37.9%) | 844 (21.3%) | 3,048 (76.9%) | 73 (1.8%) |
| M82 | 179 | 80 (44.7%) | 10 (12.5%) | 68 (85.0%) | 2 (2.5%) | 99 (54.3%) | 16 (16.2%) | 82 (82.8%) | 1 (1.0%) |
a
Intergenic region is defined as DNA sequences located between genes within the genome.
b
Genic region consists of exons and introns.
c
Exon includes the 3′-UTR, 5′-UTR, and coding regions.