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Table 2 Number of probes and targeted InDels before and after selection for array design and passing the Affymetrix® quality control according to different probes type. Percentages are indicated in brackets

From: High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array

 Before selectionOn arrayCalled by Affymetrix® pipeline
ProbesInDelaProbesInDelaProbesInDela
BP Type16,648 (0.02%)3,324 (2.82%)4,691 (0.71%)2,751 (2.6%)2,092 (0.44%)1,482 (1.66%)
BP Type251,770 (0.2%)25,885 (21.98%)38,790 (5.85%)22,662 (21.39%)20,540 (4.29%)14,407 (16.12%)
BP Type371,820 (0.27%)35,910 (30.5%)41,272 (6.23%)27,897 (26.34%)23,631 (4.93%)18,485 (20.68%)
BP Type4312 (0.001%)156 (0.13%)241 (0.04%)146 (0.14%)119 (0.02%)93 (0.1%)
OTV872,324 (3.26%)21,390 (18.16%)163,278 (24.64%)18,558 (17.52%)96,867 (20.22%)15,064 (16.85%)
MONO25,735,797 (96.25%)68,573 (58.23%)414,500 (62.54%)65,796 (62.11%)335,778 (70.1%)63,597 (71.14%)
ALL26,738,671117,756662,772105,927479,02789,393
  1. aNote that a same InDel could be genotyped by several probe types which resulted in the percentage values great than 1