Table 4 SNP filtering.
From: Fragmentation by major dams and implications for the future viability of platypus populations
Filter | Variation between groups | Variation within groups |
|---|---|---|
Reproducibility (RepAvg) | >100% | >100% |
Retain only one SNP per read | Used | Used |
Departure from Hardy-Weinberg proportions | <0.05 | <0.05 |
Mapped to chromosome | Used | Used |
BLAST alignment E-value | <1e−20 | <1e−20 |
Missing data by site | >90% | >100% |
Minor allele count (MAC) | >3 | Not used |
Linkage disequilibrium (r2) | <0.2 | Not used |
Remove sites located within coding regions | Used | Not used |
Remove sites located within sex chromosomes | Not used | Used |
Total SNPs after filtering | 2641 | 4551 |
