Recombination-aware alignment of diploid individuals

BMC Genomics

Table 2 A number of variations were applied to the reference genome, and blocks of size 200 were recombined freely.

			Synchronized diploid To diploid		Levenshtein
Length	Variations	Mutations	Distance	Time	Distance	Time
10000	100	7	7	0.006	52	0.010
20000	227	18	18	0.020	139	0.052
30000	338	33	33	0.064	241	0.138
40000	434	36	36	0.096	272	0.214
50000	538	46	46	0.140	367	0.362
60000	637	50	50	0.230	448	0.528
70000	742	67	67	0.274	529	0.850
80000	839	73	73	0.370	562	1.066
90000	960	91	91	0.550	697	1.570
100000	1089	109	109	0.688	762	2.198
1000000	10127	990	990	58.978	7676	376.320

After that, random mutations were introduced with probability 0.001. We show the distances and times (in seconds) obtained by our synchronized diploid to diploid distance algorithm and by the Levenshtein distance.

ISSN: 1471-2164