Table 2 Simulation of AFLAP testing different genome and sequencing coverage variations. Maps aligned to assemblies in Additional file 1
From: AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data
Assembly size | Chromosomes | Cross structure | Simulated progeny sequencing depth | Simulated parental sequencing depth | Simulated heterozygosity | Segregating markers detected by AFLAP | Markers used in linkage analysis | Minimum LOD score | Linkage groups calculated | Percent of markers placed in linkage groups | Collinearity of genetic map with genome assembly (average Kendall rank coefficient; Ï„) | Run time (wall clock) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
i) Altering progeny sequencing depth. | ||||||||||||
 119 Mb | 5 | F1 (ABxCC) | 20 | 50 | 0.2% | 186,522 | 10,000 | 7 | 5 | 100% | 0.993 | 8 h 44 min |
 119 Mb | 5 | F1 (ABxCC) | 10 | 50 | 0.2% | 186,523 | 10,000 | 7 | 5 | 99.8% | 0.986 | 6 h 13 min |
 119 Mb | 5 | F1 (ABxCC) | 7 | 50 | 0.2% | 186,523 | 10,000 | 7 | 5 | > 99.9% | 0.988 | 5 h 18 min |
 119 Mb | 5 | F1 (ABxCC) | 5 | 50 | 0.2% | 186,525 | 10,000 | 7 | 5 | 98% | 0.983 | 4 h 22 min |
 119 Mb | 5 | F1 (ABxCC) | 3 | 50 | 0.2% | 186,525 | 10,000 | 3 | 6 | 86.7% | 0.826 | 4 h 17 min |
ii) Altering parental sequencing depth. | ||||||||||||
 119 Mb | 5 | F1 (ABxCC) | 10 | 50 | 0.2% | 186,523 | 10,000 | 7 | 5 | 99.8% | 0.986 | 6 h 13 min |
 119 Mb | 5 | F1 (ABxCC) | 10 | 40 | 0.2% | 189,329 | 10,000 | 7 | 5 | 99.8% | 0.985 | 6 h 5 min |
 119 Mb | 5 | F1 (ABxCC) | 10 | 30 | 0.2% | 179,218 | 10,000 | 7 | 5 | 99.8% | 0.985 | 6 h 20 min |
 119 Mb | 5 | F1 (ABxCC) | 10 | 20 | 0.2% | 127,628 | 10,000 | 7 | 5 | 99.8% | 0.985 | 6 h 0 min |
 119 Mb | 5 | F1 (ABxCC) | 10 | 10 | 0.2% | 112,655 | 10,000 | 7 | 5 | 99.8% | 0.986 | 5 h 40 min |
iii) Altering parental heterozygosity. | ||||||||||||
 119 Mb | 5 | F1 (ABxCC) | 10 | 50 | 0.01% | 9996 | 9996 | 7 | 5 | 99.8% | 0.985 | 6 h 49 min |
 119 Mb | 5 | F1 (ABxCC) | 10 | 50 | 0.1% | 97,446 | 10,000 | 7 | 5 | 99.8% | 0.984 | 7 h 3 min |
 119 Mb | 5 | F1 (ABxCC) | 10 | 50 | 0.2% | 186,523 | 10,000 | 7 | 5 | 99.8% | 0.986 | 6 h 13 min |
 119 Mb | 5 | F1 (ABxCC) | 10 | 50 | 0.5% | 401,020 | 10,000 | 7 | 5 | 99.8% | 0.983 | 7 h 6 min |
 119 Mb | 5 | F1 (ABxCC) | 10 | 50 | 1% | 736,293 | 10,000 | 7 | 5 | 99.6% | 0.984 | 6 h 40 min |
 119 Mb | 5 | F1 (ABxCC) | 10 | 50 | 2% | 1,148,814 | 10,000 | 7 | 5 | 99.2% | 0.984 | 7 h 12 min |
iv) Altering genome size and chromosome number. | ||||||||||||
 119 Mb | 5 | F1 (ABxCC) | 10 | 50 | 0.2% | 186,523 | 10,000 | 7 | 5 | 99.8% | 0.986 | 6 h 13 min |
 500 Mb | 19 | F1 (ABxCC) | 10 | 50 | 0.2% | 490,397 | 50,000 | 7 | 19 | 99.2% | 0.984 | 12 h 23 min |
 900 Mb | 9 | F1 (ABxCC) | 10 | 50 | 0.2% | 801,712 | 25,000 | 7 | 9 | 99.3% | 0.982 | 22 h 0 min |
v) Altering cross type | ||||||||||||
 119 Mb | 5 | F1 (ABxCC) | 10 | 50 | 0.2% | 186,523 | 10,000 | 7 | 5 | 99.8% | 0.986 | 6 h 13 min |
 119 Mb | 5 | F2 (AAxCC) | 10 | 50 | 0% | 94,428 104,106 | 10,000 10,000 | 7 7 | 5 5 | 100% > 99.9% | 0.978 0.977 | 7 h 49 min |