Genomics and Applied Biology 2024, Vol.15, No.1, 54-63 http://bioscipublisher.com/index.php/gab 58 Table 1 Statistics of mapping analysis and detection of genome variants (SNPs) for deeper NGS genome sequences (Adopted from Ohyanagi et al., 2015) Species/Ecotype Cultivar name/NIG Wid Rice accession Number of read pairs (original) Number of read pairs (after preprocessing) Mapping analysis SNP detection Mapping rate (%, average) Mapping rate (%, read1) Mapping rate (%, read2) Average depth (x times of reference genome) Genome coverage (%) Number of SNPs(all) Number of SNPs (homogeneous) Number of SNPs (heterogeneous) Heterogeneou s ratio (%, hetero./all) Os-japonica Nipponbare (NIG stock) 27 163 585 21 977 537 85.28 94.17 76.39 9.131 89.75 12 376 4937 7439 60.11 Nongken-58 68 213 581 60 824 534 98.50 98.65 98.36 12.69 96.54 46 422 38261 8161 17.58 Os-indica Guangluai-4 54 309 982 45 105 225 92.86 93.02 92.70 15.13 90.21 1 231 216 1 145 128 86088 6.992 Os-aus Kasalath 206 469 104 199 240 404 91.53 91.54 91.51 92.39 92.84 2 020 481 1 865 985 154496 7.646 Or-I W0106 25 090 954 21 291 026 69.83 76.76 62.90 7.481 78.26 269 386 225 060 44326 16.45 W0630 79 734 147 70 417 961 90.13 90.31 89.94 32.37 89.10 2 201 911 2 053 089 148822 6.759 W1230 68 999 113 61 736 419 89.72 89.89 89.55 28.36 89.27 2 143 756 1 968 156 175600 8.191 W1921 24 756 280 21 323 134 70.03 77.36 62.69 7.086 77.87 191 542 155 355 36187 18.89 Or-II W0120 69 331 945 61 953 915 89.88 90.03 89.72 28.47 90.55 2 082 384 1 569 524 512860 24.63 W0180 63 097 081 56 313 044 88.89 89.11 88.68 25.61 89.44 1 984 170 1 629 437 354733 17.88 W1236 71 082 413 63 974 789 89.31 89.45 89.17 29.21 91.44 2 507 539 1 583 395 924144 36.85 W1715 59 688 661 53 023 455 89.84 90.03 89.64 24.36 95.20 2 776 086 974 774 1801 312 64.89 W1981 68 868 645 61 843 301 89.13 89.27 89.00 28.17 89.95 2 374 591 1 687 582 687009 28.93 Or-III W0593 72 006 505 63 695 769 88.68 88.86 88.50 28.94 88.44 2 117 072 1 963 157 153915 7.270 W1943 32 091 193 30 369 210 94.38 94.34 94.41 15.06 92.10 769 640 703 427 66213 8.603 O. longistaminata W1413 36 304 086 21 237 761 61.89 67.79 56.00 6.571 54.95 424 135 280 952 143183 33.76 W1508 15 768 341 11 679 929 66.15 68.95 63.34 3.766 51.07 305 631 198 973 106658 34.90
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