Taxon | Genome coverage (%) | Read mapped rate (%) | Variation | SNP in CDS | InDel in CDS | SNP + InDel | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Hetero SNPa | Homo SNPb | InDel | Overall | Silence | Nonsense | Missense | Splicing site | Ti/Tv | In-frame | Frame shift | Intron | Intergenic | |||
Pyn-Jeju1 | 95.4 | 94.4 | 2,838,985 | 1,096,549 | 895,813 | 4,831,347 | 148,300 | 3661 | 182,107 | 1158 | 1.56 | 4340 | 22,281 | 255,057 | 4,214,443 |
Pyn-Jeju2 | 98.6 | 95.6 | 2,596,728 | 145,287 | 764,810 | 3,506,825 | 99,482 | 2560 | 123,473 | 851 | 1.52 | 2967 | 20,894 | 180,133 | 3,076,465 |
Pyn-Jeju3 | 95.7 | 93.9 | 2,946,741 | 1,262,874 | 932,447 | 5,142,062 | 153,376 | 3679 | 187,285 | 1259 | 1.57 | 4421 | 22,453 | 269,721 | 4,499,868 |
Pyn-Jeju4 | 95.3 | 94.5 | 2,896,646 | 1,223,511 | 916,719 | 5,036,876 | 152,756 | 3652 | 186,991 | 1222 | 1.57 | 4337 | 22,262 | 266,970 | 4,398,686 |
Pyn-Jeju5 | 94.5 | 93.9 | 3,378,621 | 1,657,723 | 1,063,188 | 6,099,532 | 176,065 | 4532 | 218,722 | 1501 | 1.58 | 5187 | 23,776 | 313,087 | 5,356,662 |
Pxy-US1 | 95.0 | 94.6 | 3,464,156 | 1,629,328 | 1,072,679 | 6,166,163 | 175,976 | 4596 | 220,018 | 1527 | 1.58 | 5244 | 23,717 | 315,788 | 5,419,297 |
Pxy-US2 | 94.9 | 94.5 | 3,445,971 | 1,626,652 | 1,068,387 | 6,141,010 | 175,718 | 4600 | 219,181 | 1490 | 1.58 | 5195 | 23,653 | 314,928 | 5,396,245 |
Pxy-JP1 | 94.9 | 91.3 | 3,527,140 | 1,722,941 | 1,109,412 | 6,359,493 | 182,173 | 4620 | 225,405 | 1538 | 1.58 | 5329 | 24,706 | 324,046 | 5,591,676 |
Pxy-JP2 | 94.9 | 92.6 | 3,529,437 | 1,724,190 | 1,110,969 | 6,364,596 | 182,189 | 4639 | 225,537 | 1557 | 1.58 | 5343 | 24,780 | 324,679 | 5,595,872 |
Ppa-1 | 82.2 | 93.3 | 1,197,274 | 1,428,540 | 595,858 | 3,221,672 | 87,944 | 2581 | 116,320 | 819 | 1.60 | 2857 | 14,995 | 165,140 | 2,831,016 |
Ppa-2 | 72.0 | 94.0 | 726,505 | 1,263,932 | 482,136 | 2,472,573 | 74,707 | 1966 | 94,308 | 660 | 1.56 | 2216 | 13,013 | 136,354 | 2,149,349 |
Ppa-3 | 84.6 | 96.0 | 1,883,696 | 1,522,293 | 751,829 | 4,157,818 | 118,186 | 3088 | 148,056 | 1001 | 1.59 | 3340 | 17,363 | 218,562 | 3,648,222 |
Pjj-1 | 86.9 | 93.8 | 1,975,049 | 1,823,000 | 776,618 | 4,574,667 | 144,854 | 3306 | 173,239 | 1120 | 1.55 | 4011 | 17,776 | 238,548 | 3,991,813 |
Pjj-2 | 76.1 | 94.8 | 1,139,292 | 1,592,058 | 583,439 | 3,314,789 | 120,474 | 2333 | 138,885 | 837 | 1.52 | 3104 | 14,767 | 183,366 | 2,851,023 |
Pjq | 86.4 | 94.0 | 1,946,474 | 1,769,052 | 763,036 | 4,478,562 | 145,116 | 3211 | 172,508 | 1119 | 1.55 | 3924 | 17,563 | 233,810 | 3,901,311 |
Psa | 86.6 | 93.7 | 1,960,926 | 1,823,069 | 775,824 | 4,559,819 | 144,689 | 3312 | 173,070 | 1131 | 1.55 | 3957 | 17,591 | 240,595 | 3,975,474 |
Total | – | – | 39,453,641 | 23,310,999 | 13,663,164 | 76,427,804 | 2,282,005 | 56,336 | 2,805,105 | 18,790 | – | 65,772 | 321,590 | 3,980,784 | 66,897,422 |