Table 2 Comparison of NUMT and NUPT content between grapevine whole-genome and segmentally duplicated regions
From: Analysis of high-identity segmental duplications in the grapevine genome
| Â | Whole chromosome | Segmental duplications | ||||||
|---|---|---|---|---|---|---|---|---|
chr | NUMTs | NUPTs | NUMTs | NUPTs | ||||
| Â | 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% |