Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Table 1 SNP and indel variants detected between the B. taurus UMD3.1 reference genome and aurochs specimen CPC98

Variant type	CPC98 genotype^a	Transition or transversion	Count	Present in dbSNP 140^b	Confirmed in modern re-sequenced animals^c
SNP	Heterozygous	Transition	368,538	93.1 %	72.7 %
	Heterozygous	Transversion	166,652	91.5 %	70.0 %
	Homozygous	Transition	1,010,894	98.6 %	90.1 %
	Homozygous	Transversion	463,177	98.3 %	88.8 %
Weighted mean				96.9 %	84.9 %
Indel	Heterozygous	-	14,309	80.6 %	59.2 %
Indel	Homozygous	-	90,346	96.4 %	84.8 %
Weighted mean				94.2 %	81.3 %

^aThe CPC98 genotype is given as homozygous for positions where the CPC98 sequence is homozygous for a different allele to that in the reference genome, and heterozygous where CPC98 carries only one allele that differs from the reference
^bThe percentage of variants that are recorded in dbSNP version 140
^cThe percentage of variants that were observed in the panel of 81 sequenced modern animals

ISSN: 1474-760X