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Table 3 Comparison between the clustering expected for BP, MONO, and OTV probe types and the clustering produced by Affymetrix® pipelines based on the fluorescent intensity and contrast of 445 inbred lines for 479,027 probes

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

  Classification based on the clustering produced by Affymetrix® pipelines and genotyping assignment
Probe types BPOTV    
BPNumber (%)20,370 (43.9%)26,012 (56.1%)    
Clustering examples    
DescriptionTwo homoz. clustersTwo homoz. and one OT clusters    
  OTVMONOSNPmonomorphic  
OTVNumber (%)78,799 (81.3%)502 (0.5%)17,562 (18.1%)4 (0.0%)  
Clustering examples  
DescriptionTwo homoz. and one OT clustersOne homoz. and one OT clustersTwo homoz. clustersOne cluster  
  MONOOTVUnexpected MONO 1SNPUnexpected MONO 2monomorphic
MONONumber (%)212,434 (63,3%)15,690 (4,7%)68,562 (20,4%)1,981 (0.6%)9,525 (2.8%)27,586 (8.29%)
Clustering examples
DescriptionOne homoz. and one OT clustersTwo homoz. and one OT clustersOne homoz., one OT and one het. clustersTwo homoz. clustersOne homoz. and one het. clustersOne cluster
  1. “Clustering example”: typical example of clustering based on the fluorescent intensity (y-axis) and contrast (x-axis). Colors on figure indicate the assignation of the genotype to the individuals based on this clustering; “Number (%)”: Number (percentage) of probes displaying the corresponding clustering. “Description”: Brief characteristic of each classification based on the clustering of individuals (homoz.= homozygote, het=heterozygous, OT= off-target)