Table 1.

Summary of sequenced data and average genetic distance in each breed

Project	Sample #	Yield (Mbases)	% PF*a	# Reads	% of > = Q30 bases (PF)	Mean quality score (PF)	Genetic distance*b	1-IBS*c
Green junglefowl in Java	2	15,930	100	159,310,248	96.36	37.46	0.495	0.361
Green junglefowl in Madura	7	57,444	100	574,445,124	96.04	37.33	0.454 ± 0.01*d	0.339 ± 0.008
Red junglefowl in Sumatra	2	25,807	100	258,067,414	94.72	36.91	0.125	0.114
Red junglefowl in Java	3	24,355	100	243,545,708	95.43	37.16	0.162 ± 0.003	0.145 ± 0.002
Sumatera	5	25,432	100	254,326,066	95.13	37.04	0.164 ± 0.005	0.146 ± 0.004
Black Sumatra	10	40,056	100	400,575,800	95.1	37.05	0.171 ± 0.012	0.152 ± 0.009
Kedu Hitam	10	76,000	100	759,981,010	93.87	36.61	0.142 ± 0.010	0.128 ± 0.008
Black Java	10	86,169	100	861,690,196	91.02	35.60	0.131 ± 0.021	0.119 ± 0.017
Total/Average	49	351,193	100	3,511,941,566	94.62	36.86	0.161 ± 0.071	0.189 ± 0.105

^*a% PF means that the percentage of total number of passing filter reads per sequenced reads

^*bK2P genetic distance was calculated by Phylip

^*cIBS (Identity by state) was calculated by Tassel

^*dStandard deviation