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
Classification based on the clustering produced by Affymetrix® pipelines and genotyping assignment | |||||||
Probe types | BP | OTV | |||||
BP | Number (%) | 20,370 (43.9%) | 26,012 (56.1%) | ||||
Clustering examples |
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Description | Two homoz. clusters | Two homoz. and one OT clusters | |||||
OTV | MONO | SNP | monomorphic | ||||
OTV | Number (%) | 78,799 (81.3%) | 502 (0.5%) | 17,562 (18.1%) | 4 (0.0%) | ||
Clustering examples |
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Description | Two homoz. and one OT clusters | One homoz. and one OT clusters | Two homoz. clusters | One cluster | |||
MONO | OTV | Unexpected MONO 1 | SNP | Unexpected MONO 2 | monomorphic | ||
MONO | Number (%) | 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 |
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Description | One homoz. and one OT clusters | Two homoz. and one OT clusters | One homoz., one OT and one het. clusters | Two homoz. clusters | One homoz. and one het. clusters | One cluster | |
