------------------------------------------------------------------------------------------------------------ FILTER #SNPs #dbSNP %dbSNP Known Novel Overall %HM3 %FNR(TPR) Ts/Tv Ts/Tv Ts/Tv sites /SNP ------------------------------------------------------------------------------------------------------------ AB67 27876 2496 9.0 1.46 1.25 1.26 0.000 0.000 AB67;STR15 9167 202 2.2 1.59 0.49 0.50 0.000 0.000 AB67;str-15 9116 245 2.7 1.47 0.51 0.53 0.000 0.000 DP20000 2457 516 21.0 1.48 0.85 0.96 0.000 0.000 DP20000;AB67 2355 321 13.6 1.28 1.22 1.22 0.000 0.000 DP20000;AB67;STR15 68 11 16.2 2.67 1.04 1.19 0.000 0.000 DP20000;AB67;str-15 65 6 9.2 5.00 0.97 1.10 0.000 0.000 DP20000;STR15 209 26 12.4 0.44 0.73 0.69 0.000 0.000 DP20000;str-15 208 41 19.7 0.46 0.43 0.43 0.000 0.000 INDEL5 5513 1732 31.4 1.28 1.39 1.36 0.195 1.306 INDEL5;AB67 381 63 16.5 2.00 1.74 1.78 0.000 0.000 INDEL5;AB67;STR15 205 6 2.9 5.00 0.33 0.36 0.000 0.000 INDEL5;AB67;str-15 257 4 1.6 1.00 0.14 0.15 0.000 0.000 INDEL5;DP20000 2 1 50.0 0.00 0.00 0.00 0.000 0.000 INDEL5;DP20000;AB67 8 1 12.5 0.00 1.33 1.00 0.000 0.000 INDEL5;STR15 149 36 24.2 1.12 0.64 0.73 0.000 0.000 INDEL5;dp500 17 2 11.8 Inf 0.88 1.12 0.000 0.000 INDEL5;dp500;STR15 1 0 0.0 Inf Inf Inf 0.000 0.000 INDEL5;dp500;str-15 5 1 20.0 Inf 1.00 1.50 0.000 0.000 INDEL5;str-15 167 31 18.6 0.72 0.64 0.65 0.003 0.599 PASS 721250 190877 26.5 2.33 2.35 2.35 98.664 5.058 STR15 5581 519 9.3 1.76 0.54 0.61 0.014 0.090 dp500 737 132 17.9 1.06 1.09 1.08 0.000 0.000 dp500;AB67 13 1 7.7 0.00 3.00 2.25 0.000 0.000 dp500;AB67;STR15 6 0 0.0 Inf 0.50 0.50 0.000 0.000 dp500;AB67;str-15 8 0 0.0 Inf 0.60 0.60 0.000 0.000 dp500;STR15 168 22 13.1 1.75 0.90 0.98 0.000 0.000 dp500;str-15 199 18 9.0 1.00 1.13 1.12 0.000 0.000 q5 20945 380 1.8 2.04 2.16 2.16 0.019 0.033 q5;AB67 703 27 3.8 0.80 1.41 1.38 0.000 0.000 q5;AB67;STR15 285 1 0.4 Inf 0.35 0.36 0.000 0.000 q5;AB67;str-15 270 2 0.7 1.00 0.40 0.40 0.000 0.000 q5;DP20000 47 6 12.8 2.00 0.95 1.04 0.000 0.000 q5;DP20000;AB67 52 5 9.6 0.67 1.14 1.08 0.000 0.000 q5;DP20000;AB67;STR15 1 0 0.0 Inf 0.00 0.00 0.000 0.000 q5;INDEL5 167 18 10.8 1.25 1.40 1.39 0.000 0.000 q5;INDEL5;AB67 10 1 10.0 Inf 2.00 2.33 0.000 0.000 q5;INDEL5;AB67;STR15 7 0 0.0 Inf 1.33 1.33 0.000 0.000 q5;INDEL5;AB67;str-15 9 0 0.0 Inf 0.50 0.50 0.000 0.000 q5;INDEL5;STR15 12 0 0.0 Inf 1.00 1.00 0.000 0.000 q5;INDEL5;str-15 10 1 10.0 0.00 1.25 1.00 0.000 0.000 q5;STR15 333 6 1.8 0.50 0.39 0.39 0.000 0.000 q5;dp500 54 2 3.7 1.00 1.89 1.84 0.000 0.000 q5;dp500;AB67 1 0 0.0 Inf Inf Inf 0.000 0.000 q5;dp500;STR15 7 0 0.0 Inf 1.33 1.33 0.000 0.000 q5;dp500;str-15 10 1 10.0 0.00 0.80 0.67 0.000 0.000 q5;str-15 349 1 0.3 0.00 0.30 0.30 0.000 0.000 str-15 6252 886 14.2 1.89 0.63 0.74 0.024 0.144 ------------------------------------------------------------------------------------------------------------ FILTER #SNPs #dbSNP %dbSNP Known Novel Overall %HM3 %FNR(TPR) Ts/Tv Ts/Tv Ts/Tv sites /SNP ------------------------------------------------------------------------------------------------------------ AB67 50863 3392 6.7 1.46 0.87 0.90 0.000 0.000 DP20000 5472 934 17.1 1.30 0.98 1.03 0.000 0.000 INDEL5 6920 1897 27.4 1.29 1.17 1.20 0.197 1.055 PASS 721250 190877 26.5 2.33 2.35 2.35 98.664 5.058 STR15 16199 829 5.1 1.62 0.51 0.54 0.014 0.031 dp500 1226 179 14.6 1.13 1.10 1.10 0.000 0.000 q5 23272 451 1.9 1.78 1.91 1.91 0.019 0.030 str-15 16925 1237 7.3 1.64 0.54 0.59 0.027 0.059 ------------------------------------------------------------------------------------------------------------ PASS 721250 190877 26.5 2.33 2.35 2.35 98.664 5.058 FAIL 94462 7770 8.2 1.47 1.04 1.07 0.254 0.100 TOTAL 815712 198647 24.4 2.29 2.08 2.12 98.918 4.484 ------------------------------------------------------------------------------------------------------------