Fig 1.
Summary of the heterogeneity, minor allele frequency (MAF) and polymorphic information content (PIC) of 18,082 selected SNPs.
Chromosome assignments are indicated; where no BLAST position was available, the chromosome is designated as “0”; The heterogeneity, MAF, percentage of Missing value, PIC was shown in left y-axis, the number of marker for each chromosome was shown in right y-axis.
Fig 2.
Analysis of methods to enable selection of markers for QC genotyping.
a: MAF effect. Random selection (Random); MAF < 0.15 (0.05–0.15); MAF between 0.15 and 0.25 (0.15–0.25); MAF > 0.25 (>0.25); b: Marker Group effect on select marker for QC. Random selection (Random); Same percentage of marker from each marker group (PG); same number of markers selected from each group (NG); Keep the proportion of each group distance (PGD). c: Marker coverage effect. Random selection (Random); Coverage < 2 (0–2); Coverage between 2 and 15 (2–15); Coverage >15 (>15). d: Marker distribution effect. Standard error bars are shown.
Fig 3.
Association analysis indentifies QPM and imidazolinone resistance markers.
Fig 4.
Comparison of the effect of the final marker selection rules versus random marker selection on the proportion of CML pairs not distinguished from one another.
Fig 5.
Comparison of five subsets of SNPs for broad QC and rapid QC.
a: Five subsets of 80 SNPs for broad QC genotyping; b: Five subsets of 10 SNPs for rapid QC genotyping.
Table 1.
Similarity between original CMLs and re-generation using 80 broad QC markers.
Genotypic similarity is indicated in parentheses.
Table 2.
Similarity between original CMLs and different re-generation using 10 rapid QC markers.
Genotypic similarity is indicated in parentheses.
Fig 6.
Probability of detecting at least one off-type using different sample sizes at different assumed off-type levels (P) within populations.