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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; τ) 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