Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

Table 1 Sequencing libraries and sequencing runs

Library	Run name	Read length	F3 reads	R3 reads
Black Angus FR 50	solid_BA_FR1	50 nt	172,104,943	0
Black Angus FR 50	solid_BA_FR2	50 nt	225,062,253	0
Black Angus MP 25	solid_BA_MP1	25 nt	73,568,858	73,917,320
Black Angus MP 25	solid_BA_MP2	25 nt	76,123,158	76,573,521
Black Angus MP 25	solid_BA_MP3	25 nt	69,657,261	69,108,403
Black Angus MP 25	solid_BA_MP4	25 nt	356,566,421	356,848,504
Black Angus MP 50	solid_BA_MP5	50 nt	220,164,958	220,910,123
Black Angus MP 50	solid_BA_MP6	50 nt	78,350,806	80,494,794
Black Angus MP 50	solid_BA_MP7	50 nt	343,878,503	346,998,757
Holstein MP 50	solid_HOL_MP1	50 nt	140,503,099	142,438,241
Holstein MP 50	solid_HOL_MP2	50 nt	190,712,998	191,191,811
Holstein FR 50	solid_HOL_FR1	50 nt	172,127,298	0
Holstein FR 50	solid_HOL_FR2	50 nt	321,848,214	0
Holstein MP 25	solid_HOL_MP3	25 nt	160,118,556	159,430,437
Holstein MP 25	solid_HOL_MP4	25 nt	281,714,461	281,402,729

Three libraries were constructed for each animal and sequenced using two or more instrument runs. The numbers of reads obtained for fragment libraries is given in the F3 reads column. Mate-paired libraries yielded two read types (F3 reads and R3 reads).