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Table 1 Summary of sequenced data and average genetic distance in each breed

From: Genetic features of red and green junglefowls and relationship with Indonesian native chickens Sumatera and Kedu Hitam

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
  1. *a% PF means that the percentage of total number of passing filter reads per sequenced reads
  2. *bK2P genetic distance was calculated by Phylip
  3. *cIBS (Identity by state) was calculated by Tassel
  4. *dStandard deviation
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