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Table 2 Comparison of copy number calls at variant regions

From: A comparison of genomic copy number calls by Partek Genomics Suite, Genotyping Console and Birdsuite algorithms to quantitative PCR

CN 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4
  Region 1 Region 2 Region 3
  Chr2:242,648,367 Chr3:53,010,599 Chr7:133,441,893
Partek 0b 4 24 0 0 0 1 24 0 0 0 1 5 0 0
GTC 0 4 24 0 0 1 3 21 0 0 0 1 4 1 0
Birdsuite 0 4 24 0 0 1 3 21 0 0 1 3 2 0 0
qPCR 0 4 24 0 0 1 3 21 0 0 1 3 2 0 0
  Region 4 Region 5 Region 6
  Chr8:144,776,429 Chr19:56,824,268 Chr19:56,838,253
Partek 0 0 8 0 0 0 0 13 13 0 0 0 7 6 0
GTC 1 0 7 0 0 0 0 17 3 6 0 0 6 3 4
Birdsuite 1 2 5 0 0 0 0 26 0 0 0 2 11 0 0
qPCR 1 2 5 0 0 1 6 19 0 0 0 2 11 0 0
  Region 7 Region 8 Region 9
  Chr20:1,522,539 Chr22:22,643,636 Chr22:22,713,888
Partek 0 4 13 7 0 0 0 23 5 0 0 0 14 12 0
GTC 0 4 13 0 7 1 0 24 3 0 1 1 16 6 2
Birdsuite 17 7 0 0 0 12 11 5 0 0 2 13 11 0 0
qPCR 18 6 0 0 0 0 0 28 0 0 2 14 10 0 0
  1. aGTC = Genotyping Console 2.0
  2. bValues are numbers of samples called each copy number at each region.
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