Table 1 Nicotiana genome assembly metrics
N. rustica | N. undulata | N. paniculata | N. knightiana | |
|---|---|---|---|---|
Coverage | 90x | 122x | 100x | 82x |
Contigs | 863,445 | 240,808 | 289,247 | 368,273 |
Scaffolds | 246,567 | 117,559 | 181,973 | 160,417 |
Average scaffold length | 18,053 | 16,284.2 | 12,038.2 | 14,331.7 |
Longest scaffold | 709,624 | 435,587 | 551,851 | 749,769 |
N50 length | 84,603 | 61,881 | 52,808 | 82,722 |
E-size | 106,321.7 | 76,855.5 | 68,024.3 | 103,550.5 |
Assembly length | 4,451,279,893 | 1,914,350,984 | 2,190,627,570 | 2,299,051,887 |
Undefined bases | 458,861,024 (10.31%) | 15,815,547 (0.83%) | 2,994,201 (0.14%) | 47,367,942 (2.06%) |
Genome size (KMER) [Gb] | 4.99 | 2.18 | 3.26 | 3.12 |
Genome size (KEW) [Gb] | 5.181 | 2.362 | 2.88 | 3.09 |
Genome coverage (KMER) | 0.892 | 0.878 | 0.672 | 0.737 |
Genome coverage (KEW) | 0.8591 | 0.81 | 0.761 | 0.744 |
genes and regulatory sequences | 956,876,918 (24%) | 469,801,265 (25%) | 487,609,360 (22%) | 513,178,366 (23%) |
DNA transposons | 107,092,333 (3%) | 56,581,894 (3%) | 55,826,622 (3%) | 55,840,784 (2%) |
LTR elements | 1,747,332,959 (44%) | 820,008,945 (43%) | 981,515,044 (45%) | 1,014,595,360 (45%) |
Retrotransposons | 532,753,114 (13%) | 243,526,350 (13%) | 303,566,434 (14%) | 304,961,922 (14%) |
Non-LTR retroelements (SINES, LINES) | 30,145,844 (1%) | 15,712,962 (1%) | 15,526,693 (1%) | 15,258,713 (1%) |
Others (Satellites, unknown, low complexity) | 618,217,701 (15%) | 292,904,021 (15%) | 343,589,216 (16%) | 347,848,800 (15%) |