Table 2 Effect of minimum read length filtering and trimming the ends of minION reads on heterozygosity and accuracy across the all DH samples, filtered for between 2 and 5 supporting reads.
DP 2–5 genotype calls | None | >500 bp reads | >1 kbp reads | >4 kbp reads | 100 bp ends trimmed |
|---|---|---|---|---|---|
Average nr of comparable SNPs per individual | 779,184 | 776,426 | 770,463 | 708,370 | 759,754 |
Discrepant with Illumina % | 8.3 | 8.4 | 8.4 | 8.4 | 8.4 |
Concordant with Illumina % | 91.7 | 91.6 | 91.6 | 91.6 | 91.6 |
Heterozygous in minION % | 4.2 | 4.2 | 4.2 | 4.2 | 4.2 |
Homozygous genotype calls | |||||
Discrepant with Illumina % | 5.3 | 5.3 | 5.3 | 5.4 | 5.3 |
Concordant with Illumina % | 94.7 | 94.7 | 94.7 | 94.6 | 94.7 |
