Table 2 |
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|
Comparison of NUMT and NUPT content between grapevine whole-genome and segmentally duplicated regions |
||||||||
|
Whole chromosome |
Segmental duplications |
|||||||
|
|
||||||||
|
chr |
NUMTs |
NUPTs |
NUMTs |
NUPTs |
||||
|
|
||||||||
|
bp |
percentage |
bp |
percentage |
bp |
percentage |
bp |
percentage |
|
|
|
||||||||
|
chr1 |
35,148 |
0.15% |
31,915 |
0.14% |
7,942 |
0.29% |
2,216 |
0.08% |
|
chr2 |
23,352 |
0.12% |
37,460 |
0.20% |
5,029 |
0.17% |
16,919 |
0.56% |
|
chr3 |
46,530 |
0.24% |
21,546 |
0.11% |
3,746 |
0.10% |
1,888 |
0.05% |
|
chr4 |
40,855 |
0.17% |
26,304 |
0.11% |
8,651 |
0.26% |
2,803 |
0.08% |
|
chr5 |
36,974 |
0.15% |
25,890 |
0.10% |
6,936 |
0.19% |
2,263 |
0.06% |
|
chr6 |
42,918 |
0.20% |
35,543 |
0.17% |
14,186 |
0.50% |
10,820 |
0.38% |
|
chr7 |
29,780 |
0.14% |
29,239 |
0.14% |
1,282 |
0.05% |
2,409 |
0.10% |
|
chr8 |
52,538 |
0.23% |
38,971 |
0.17% |
16,355 |
0.81% |
10,005 |
0.49% |
|
chr9 |
40,017 |
0.17% |
41,931 |
0.18% |
12,529 |
0.22% |
13,459 |
0.24% |
|
chr10 |
40,034 |
0.22% |
29,263 |
0.16% |
6,255 |
0.18% |
9,896 |
0.29% |
|
chr11 |
32,762 |
0.17% |
40,550 |
0.20% |
8,227 |
0.38% |
8,354 |
0.39% |
|
chr12 |
79,290 |
0.35% |
42,133 |
0.19% |
46,728 |
1.07% |
11,608 |
0.27% |
|
chr13 |
59,784 |
0.25% |
40,806 |
0.17% |
22,390 |
0.49% |
12,465 |
0.27% |
|
chr14 |
59,292 |
0.20% |
32,831 |
0.11% |
12,094 |
0.27% |
5,976 |
0.13% |
|
chr15 |
25,964 |
0.13% |
25,086 |
0.12% |
5,899 |
0.13% |
4,076 |
0.09% |
|
chr16 |
55,547 |
0.25% |
41,895 |
0.19% |
21,245 |
0.38% |
10,531 |
0.19% |
|
chr17 |
26,574 |
0.16% |
28,029 |
0.16% |
3,702 |
0.15% |
2,812 |
0.11% |
|
chr18 |
60,444 |
0.21% |
40,038 |
0.14% |
22,523 |
0.49% |
8,360 |
0.18% |
|
chr19 |
39,838 |
0.17% |
30,991 |
0.13% |
12,876 |
0.22% |
6,879 |
0.12% |
|
Tot_nonrandom |
827,641 |
0.19% |
640,421 |
0.15% |
238,595 |
0.33% |
143,739 |
0.20% |
|
chr1_random |
1,763 |
0.31% |
2,762 |
0.49% |
78 |
0.06% |
33 |
0.02% |
|
chr3_random |
872 |
0.07% |
1,082 |
0.09% |
0 |
0.00% |
0 |
0.00% |
|
chr4_random |
0 |
0.00% |
0 |
0.00% |
- |
- |
- |
- |
|
chr5_random |
642 |
0.15% |
366 |
0.09% |
- |
- |
- |
- |
|
chr7_random |
2,355 |
0.16% |
2,195 |
0.15% |
352 |
0.25% |
55 |
0.04% |
|
chr9_random |
525 |
0.11% |
81 |
0.02% |
93 |
0.07% |
0 |
0.00% |
|
chr10_random |
111 |
0.01% |
1,096 |
0.14% |
0 |
0.00% |
0 |
0.00% |
|
chr11_random |
667 |
0.24% |
191 |
0.07% |
- |
- |
- |
- |
|
chr12_random |
1,522 |
0.10% |
2,588 |
0.17% |
674 |
0.17% |
1,756 |
0.43% |
|
chr13_random |
8,607 |
0.26% |
5,168 |
0.16% |
4,914 |
0.46% |
2,903 |
0.27% |
|
chr16_random |
636 |
0.09% |
977 |
0.13% |
636 |
0.09% |
977 |
0.15% |
|
chr17_random |
94 |
0.01% |
770 |
0.09% |
0 |
0.00% |
0 |
0.00% |
|
chr18_random |
5,302 |
0.10% |
3,476 |
0.07% |
2,709 |
0.20% |
509 |
0.04% |
|
Tot_random |
23,096 |
0.14% |
20,752 |
0.12% |
9,456 |
0.20% |
6,233 |
0.13% |
|
Tot_placed |
850,737 |
0.19% |
661,173 |
0.15% |
248,051 |
0.33% |
149,972 |
0.20% |
|
chrUn |
417,301 |
0.97% |
69,457 |
0.16% |
159,039 |
1.79% |
21,834 |
0.25% |
|
Tot_whole |
1,268,038 |
0.26% |
730,630 |
0.15% |
407,090 |
0.48% |
171,806 |
0.20% |
|
|
||||||||
|
Giannuzzi et al. BMC Genomics 2011 12:436 doi:10.1186/1471-2164-12-436 |
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