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
|
- aHeterozygous SNP rate, proportion of heterozygous SNPs in a genome
- bHomozygous SNP rate, proportion of homozygous SNPs in a genome
- Ti transition, Tv transversion