Table II. Metrics for four separate runs of IGGPIPE on S. lycopersicum/S. pennellii genomes using four different sets of parameters.
Note how the initial unique k-mer pool (metric unique k-mers) is filtered down at each step of IGGPIPE until finally converging at nonoverlapping validated candidate IGG markers. Each run uses a different marker identifier prefix to distinguish the markers. The IGG markers from these runs are provided (Supplemental Data S1). The metrics k, KMIN, AMIN, AMAX, ADMIN, and ADMAX are all user-specified parameters.
| Metric | Run 1 (A) | Run 2 (B) | Run 3 (C) | Run 4 (D) |
|---|---|---|---|---|
| Marker identifier prefix (ID_PREFIX) | IGG_HP14A_ | IGG_HP14B_ | IGG_HP14C_ | IGG_HP14D_ |
| Genome 1 | S. lycopersicum SL2.50 | Same | Same | Same |
| Genome 2 | S. pennellii V2.0 | Same | Same | Same |
| k | 14 | Same | Same | Same |
| Genome size (No. of k-mers) | 824/990 Mb | Same | Same | Same |
| Unique k-mers | 24.7/23.9 M | Same | Same | Same |
| Common unique k-mers | 8.9 M | Same | Same | Same |
| Minimum k-mers per LCR (KMIN) | 4 | 2 | 4 | 2 |
| Minimum amplicon size (AMIN) | 200 | 250 | 300 | 400 |
| Maximum amplicon size (AMAX) | 700 | 800 | 800 | 1,500 |
| Minimum amplicon size difference at AMIN (ADMIN) | 100 | 100 | 200 | 50 |
| Minimum amplicon size difference at AMAX (ADMAX) | 100 | 200 | 200 | 300 |
| LCRs | 102 K | 106 K | 90.4 K | 72.5 K |
| Nonoverlapping Indel Groups | 11 K | 9.2 K | 5.0 K | 32 K |
| Overlapping Indel Groups | 333 K | 31.3 K | 113 K | 250 K |
| Overlapping unvalidated markers | 26.6 K | 11.7 K | 9.3 K | 97.6 K |
| Overlapping e-PCR-validated IGG markers | 21,654 | 9,437 | 7,163 | 91,947 |
| Nonoverlapping e-PCR-validated IGG markers | 5,526 | 3,720 | 2,332 | 16,442 |