Table 5.
SNP annotation
| Soybean line | Jack | FAM94-41 | M23 | N0304-303-3 | R02-6268 F | R05-4256 | R05-591 | R08-1450 | R95-1705 | Total | Average |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Total SNP count in annotated genes |
15,752 |
27,123 |
24,906 |
24,909 |
26,504 |
19,308 |
21,040 |
28,962 |
24,518 |
48,792 |
23,669 |
| Average read depth per SNP |
13 |
17 |
15 |
14 |
20 |
12 |
15 |
21 |
15 |
- |
16 |
| Total length of annotated transcripts covered (in nt) |
49,680,448 |
54,713,084 |
53,001,316 |
49,673,932 |
57,245,339 |
49,901,790 |
55,367,363 |
51,984,636 |
51,682,304 |
|
|
| SNPs overlapping with dbSNP |
12,748 |
22,182 |
20,494 |
20,380 |
21,741 |
15,598 |
17,082 |
23,828 |
20,048 |
39,998 |
19,345 |
| SNPs in annotated exons |
14,271 |
23,757 |
22,450 |
22,311 |
23,202 |
17,023 |
18,333 |
25,381 |
21,544 |
43,283 |
20,919 |
| SNPs in annotated UTRs |
4,156 |
7,226 |
6,659 |
6,657 |
6,939 |
5,082 |
5,533 |
7,644 |
6,479 |
12,748 |
6,264 |
| SNPs in annotated CDS |
10,115 |
16,531 |
15,791 |
15,654 |
16,263 |
11,941 |
12,800 |
17,737 |
15,065 |
30,535 |
14,655 |
| Non-synonymous SNPs |
4,759 |
7,814 |
7,441 |
7,338 |
7,769 |
5,704 |
6,113 |
8,383 |
7,271 |
14,372 |
6,955 |
| Synonymous SNPs |
5,365 |
8,731 |
8,366 |
8,329 |
8,512 |
6,250 |
6,704 |
9,372 |
7,808 |
16,196 |
7,715 |
| SNPs eliminating start codons |
6 |
11 |
9 |
8 |
8 |
7 |
7 |
12 |
6 |
17 |
9 |
| SNPs causing premature termination codons |
29 |
70 |
68 |
67 |
80 |
44 |
44 |
72 |
55 |
125 |
59 |
| SNPs eliminating termination codons |
24 |
28 |
29 |
31 |
30 |
21 |
23 |
29 |
28 |
49 |
27 |
| SNPs in splice sites |
220 |
369 |
342 |
323 |
354 |
245 |
254 |
357 |
313 |
606 |
309 |
| SNPs in annotated introns | 2,120 | 4,483 | 3,469 | 3,609 | 4,377 | 3,036 | 3,575 | 4,752 | 3,957 | 7,488 | 3,709 |