TABLE 2.
Summary of Mistassini Lake walleye sequence statistics after each stage of filtering using stacks. Loci identified here are stacks loci
| After cutadapt, loaded into process_radtags, total sequences | After process_radtags, retained reads, number (percentage) | After ustacks filtering: average (min, max) | sstacks_rx | populations_rx (all rivers and years considered separately, no positive controls, samples of unknown origin removed) | |
|---|---|---|---|---|---|
| Plate 1 | 364,678,780 | 322,853,622 (88.5%) | NA | NA | NA |
| Plate 2 | 374,785,960 | 334,978,264 (89.4%) | NA | NA | NA |
| Plate 3 | 347,655,212 | 297,199,476 (85.5%) | NA | NA | NA |
| Plate 4 | 408,731,443 | 360,381,408 (88.2%) | NA | NA | NA |
| Number of reads per individual (for 371 individuals) | NA | average 3,478,507, STDEV (1,624,881) | 2,617,476 (175,372, 7,342,579) | NA | NA |
| Depth of coverage per individual | NA | NA | 23.8 (7, 677) | NA | NA |
| Number of loci | NA | NA | NA | 244,712 | 50,319 |
| Number of SNPs | NA | NA | NA | NA | 8,728 |
| Mean depth of coverage for each SNP across all individuals | NA | NA | NA | NA | 26 (STDEV 14, min 7, max 118) |
“rx” appended to the program module name indicates that the statistic presented was at the end of the analysis completed by that module, following log‐likelihood filtering and correction using rx_stacks