Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring

BMC Genomics

Table 3 Nucleotide diversity (π) based on coding sequences (CDS) of CLM2 and IFIT10 genes

Genes	CDS length (bp)	π (long reads)^c	π (short reads)^d
CLM2B1	738^a	0.054 (3)	0.015
CLM2B2	690	0.031 (4)	0.027
CLM2C	696	0.014 (4)	0.012
IFIT10A	1440	0.031 (4)	0.064
IFIT10B	1374^b	0.001 (2)	0.046

^aOne sequence is 741 bp and three are 738 bp
^bIFIT10B in CS5_h2 is 1370 bp and has a 4 bp deletion compared with other sequences
^cNucleotide diversity calculated using sequences extracted from PacBio assemblies from CS4 and CS5 samples. The number of sequences used in the π calculation is given in parentheses and indicates the copies with complete coding sequences, excluding truncated copies
^dNucleotide diversity calculated using the same samples based on short-read data with pixy [29] and the AllSites VCF file

ISSN: 1471-2164