Investigating the impact of reference assembly choice on genomic analyses in a cattle breed

BMC Genomics

Table 1 Mapping statistics for the 161 BSW samples

Parameter	Unit	ARS-UCD1.2	UOA_Angus_1
Autosomal reads	Million	47,502	47,128
	Million / sample	295 ± 131	293 ± 130
Autosomal high-quality reads	Million	42,418	42,029
	Million / sample	263 ± 118	261 ± 117
	% / sample	89.28 ± 5.06	89.17 ± 5.06
	% / chromosome	89.28 ± 0.34	89.17 ± 0.56
Coverage	fold / sample	14.13 ± 7.26	14.11 ± 7.25
	fold / chromosome	14.13 ± 0.14	14.11 ± 0.15

Summary statistics extracted from the BAM files after aligning the samples to either the ARS-UCD1.2 or UOA_Angus_1 assembly. Uniquely mapped and properly paired reads with MQ >10 are considered as high-quality reads. The percentage of autosomal reads that are high-quality reads is calculated per sample and per chromosome. Coverage of high-quality reads is calculated per sample and per chromosome

ISSN: 1471-2164