Characterisation of a transcriptome to find sequence differences between two differentially migrating subspecies of the willow warbler Phylloscopus trochilus

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.

ISSN: 1471-2164