Table 2.
Sequencing depth and SNP statistics for different features
| Feature | Number of bp | Mean sequencing depth (range) | Number of SNPs | SNP density (SNPs/1000 bp) |
|---|---|---|---|---|
|
All |
69,789,646 |
6.4 (1–3,148) |
162,503 |
10.7 |
|
Intergenic |
37,264,390 |
5.9 (1–3,148) |
102,217 |
12.3 |
|
Genic |
32,525,078 |
7.0 (1–1,738) |
60,286 |
8.8 |
| Exon |
9,872,566 |
15.6 (1–1,738) |
36,254 |
8.5 |
| Intron | 21,373,444 | 3.0 (1–561) | 20,604 | 9.3 |
SNPs refer to high-quality SNPs (minor allele frequency ≥ 0.05 and the minor allele present in at least three reads). SNP density was calculated by dividing the number of SNPs with the number of positions with a minimum sequencing depth of six reads, which is the lowest depth in which a SNP can be detected using the filtering requirements.