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Table 2 CNVR numbers, lengths and coverage for each CNV detection method used

From: Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances

Software Copy state Na CNVR length (bp) Total (Mb) Coverage (%)b
Mean Median Min Max
Brown Swiss
PennCNV Loss 210 51,633.0 24,514.5 1358 483,799 10.843 0.43
Gain 66 84,062.2 24,387.5 2809 1,879,682 5.548 0.22
Both 30 241,581.7 104,390.5 7538 1,347,298 7.247 0.29
Overall 306      23.638 0.94
SVS Loss 141 41,221.0 6858.0 1086 1,217,387 5.812 0.23
Both 46 37,702.4 10,232.5 1774 353,135 1.734 0.07
Overall 187      7.546 0.30
Consensus Loss 9 42,871.3 47,761.0 4693 90,545 0.386 0.02
Both 21 197,095.7 53,252.0 1404 945,913 4.139 0.16
Overall 30      4.525 0.18
Tyrol Grey
PennCNV Loss 502 95,870.1 49,568.0 1358 2,611,715 48.127 1.65
Gain 90 47,216.2 24,954.0 2455 279,361 4.249 0.15
Both 14 518,196.6 256,469.0 5035 1,646,040 7.255 0.25
Overall 606      59.631 2.04
SVS Loss 115 167,013.8 11,531.0 1369 4,210,187 19.207 0.66
Both 38 44,509.8 11,567.0 1774 652,218 1.691 0.06
Overall 153      20.898 0.72
Consensus Loss 49 142,561.0 75,065.0 3620 1,432,454 6.985 0.24
Both 22 205,619.5 58,194.5 2270 790,623 4.524 0.16
Overall 71      11.509 0.39
Pinzgauer
PennCNV Loss 390 63,906.2 26,759.5 1300 951,876 24.923 0.99
Gain 100 35,733.7 20,985.5 1950 279,361 3.573 0.14
Both 38 373,093.4 164,810.5 4038 2,050,695 14.17755 0.56
Overall 528      42.67433 1.70
SVS Loss 119 66,791.9 8018.0 1169 1,311,740 7.94824 0.32
Gain 1 307,583.0 307,583.0 307,583 307,583 0.307583 0.01
Both 58 31,875.8 10,004.5 1369 320,050 1.848796 0.07
Overall 178      10.10462 0.40
Consensus Loss 17 66,484.7 31,556.0 4895 459,485 1.13024 0.05
Both 33 179,520.3 34,711.0 1774 947,366 5.924169 0.24
Overall 50      7.054409 0.28
  1. aN = Number of CNVRs
  2. bThe coverage percentage is based on the bovine autosomal genome size of 2511 Mb covered by the BovineHD SNP chip
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