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example_input_output_files.Md

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Example input file

(can also deal with commented lines/locus names in the first two rows)

1.6 -9  3 2  2 -9 2 -9 -9 -9  0  1 1  3 3 1 -9 2 2  0 -9  0  0  3 3  3  2  2  1 -9 1  2 1  2  0  3  2  0 2 3
1.6 -9  3 2  2 -9 0 -9 -9 -9  0  1 1  3 3 1 -9 2 2  0 -9  0  0  3 3  3  1  2  1 -9 1  2 1  2  0  3  2  0 0 3
1.Lpry -9  1 2 -9 -9 0 -9 -9 -9 -9 -9 1  3 3 1  1 2 2 -9 -9  0  0 -9 3 -9 -9 -9  1  0 1 -9 1 -9  0 -9 -9  0 2 3 
1.Lpry -9  1 2 -9 -9 0 -9 -9 -9 -9 -9 1  3 3 1  1 2 2 -9 -9  0  0 -9 3 -9 -9 -9  1  0 1 -9 0 -9  0 -9 -9  0 2 3 
10.Lpry  3  1 2  2  2 0  2  3  3  0  1 1  3 3 1  1 2 2  0  1  0  0  1 3  3  2  2  1  0 1  2 1  2  0  3  2  0 2 3
10.Lpry  3  1 2  2  2 0  2  3  3  0  1 1  3 3 1  1 2 2  0  1  0  0  3 3  3  2  3  1  0 1  2 0  2  0  3  2  0 2 3
11.Lpry -9 -9 2  2 -9 0 -9 -9  3 -9  1 1  3 3 1  1 2 2  3 -9  0 -9 -9 3  3  2  3  1 -9 1  2 1  2  0 -9  2  0 2 3
11.Lpry -9 -9 2  2 -9 0 -9 -9  3 -9  1 1  3 3 1  1 2 2  3 -9  0 -9 -9 3  3  2  3  1 -9 1  2 1  2  0 -9  2  0 2 3
15.Lpry -9  1 2  2 -9 0 -9 -9 -9 -9 -9 1  3 3 1  1 2 2  0 -9  0  0 -9 3  3  2 -9  1  0 1  2 1  2  2 -9  2  0 2 3
15.Lpry -9  1 2  2 -9 0 -9 -9 -9 -9 -9 1  3 3 1  1 2 2  0 -9  0  0 -9 3  3  2 -9  1  0 1  2 0  2  0 -9  2  0 2 3
16.Lpry -9  1 2  2 -9 0 -9 -9 -9 -9  1 1  3 3 1  1 2 2  0 -9  2  0 -9 3  2  2  3  1 -9 1  2 1  2  0 -9  2  2 2 3
16.Lpry -9  1 2  2 -9 0 -9 -9 -9 -9  1 1  3 3 1  1 2 2  0 -9  0  0 -9 3  3  2  3  1 -9 1  2 1  2  0 -9  2  0 2 3
17.Lpry  3 -9 2 -9  2 2  2  3 -9  0  1 1  2 3 1 -9 2 2  0 -9 -9  0 -9 3  3 -9 -9  1  0 1  2 1  2  0 -9  2  0 2 3
17.Lpry  3 -9 2 -9  2 0  2  3 -9  0  1 1  3 3 1 -9 2 2  0 -9 -9  0 -9 3  3 -9 -9  1  0 1  2 0  0  0 -9  2  0 2 3
18.Lpry -9  1 2 -9 -9 0 -9 -9 -9 -9 -9 1  3 3 1 -9 2 2  3 -9  0  0 -9 3  3  2  2  1  0 1 -9 0 -9  0 -9  2  2 2 3
18.Lpry -9  1 2 -9 -9 0 -9 -9 -9 -9 -9 1  3 3 1 -9 2 2  3 -9  0  0 -9 3  3  2  2  1  0 1 -9 0 -9  0 -9  2  0 2 3
2.5 -9  1 2 -9 -9 0 -9 -9 -9 -9  1 1  3 3 1  1 2 2  0 -9  0  0 -9 3  3  2  2  1  1 1 -9 1  2  0 -9  2  0 2 3
2.5 -9  1 2 -9 -9 0 -9 -9 -9 -9  1 1  3 3 1  1 2 2  0 -9  0  0 -9 3  3  1  3  1  1 1 -9 1  2  0 -9  2  0 2 3
2.Lpry -9  1 2  2 -9 2 -9 -9  3  0  1 1  3 3 1  1 2 2  0 -9  0  0 -9 3  3  2  3  1  1 1  2 1  2  0 -9  2  0 2 3 
2.Lpry -9  1 2  2 -9 0 -9 -9  0  0  1 1  3 3 1  1 2 2  0 -9  0  0 -9 3  3  2  3  1  1 1  2 0  2  0 -9  2  0 2 3 
3.Lpry -9  1 2  2 -9 0 -9 -9 -9  0  1 1  3 3 1  1 2 2  3 -9  0  0  3 3  3  2  3  1 -9 1  2 1  2  0 -9  2  2 2 3 
3.Lpry -9  1 2  2 -9 0 -9 -9 -9  0  1 1  3 3 1  3 2 2  0 -9  0  0  3 3  3  1  3  1 -9 1  2 1  2  0 -9  2  2 2 3

Example output

sample1	sample2	total_SNPs	mismatched_SNPs	mismatch_perc	mismatch_both_hets	both_hets_perc	mismatch_both_homs	non_both_hets_both_homs_perc	mismatch_het_hom	non_both_hets_perc_het_hom
1.6	1.Lpry	8604	569	6.61	0	0	81	14.24	488	85.76
1.6	10.Lpry	13288	1162	8.74	0	0	228	19.62	934	80.38
1.6	11.Lpry	13675	1232	9.01	1	0.08	244	19.81	987	80.11
1.6	12.Lpry	13033	1196	9.18	0	0	237	19.82	959	80.18
1.6	13.Lpry	13079	1196	9.14	1	0.08	223	18.65	972	81.27
1.6	14.Lpry	13273	1105	8.33	2	0.18	204	18.46	899	81.36