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Table 4 Summary of SNP and InDel variations in Prunus species

From: Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

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
  1. aHeterozygous SNP rate, proportion of heterozygous SNPs in a genome
  2. bHomozygous SNP rate, proportion of homozygous SNPs in a genome
  3. Ti transition, Tv transversion
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