Table 2.
Genomics statistics.
| Sequencing data | 2 C | A41 | VS | VT | C3 | SP |
|---|---|---|---|---|---|---|
| SRA codes | SRR1914377; SRR1914378 | SRR1826176; SRR1826114; SRR1914331 | SRP055806 | SRP055806 | SRR1826175; SRR1825940; SRR1914330 | SRP055806 |
| Number of raw reads | — | 90,410,254 (×2) | 148,872,150 (×2) | 129,452,237 (×2) | 126,585,508 (×2) | 174,120,908 (×2) |
| Number of reads | — | 88,593,112 (×2) | 138,616,098 (×2) | 121,283,190 (×2) | 123,535,166 (×2) | 163,030,615 (×2) |
| Total amount sequence (Gb) | — | 110 | 82,1 | 64 | 46 | 93,6 |
| Estimated fold coverage | — | 24.6× | 38.5× | 33.7× | 34.3× | 45.3× |
| ABySS assembly | ||||||
| Number of contigs | — | 5,741,441 | 6,988,492 | 6,242,434 | 8,456,162 | 7,566,149 |
| Total length (contigs, Mb) | — | 1,106.4 | 1,001.4 | 922.1 | 1,409.1 | 1,116.3 |
| IMR-DENOM reconstruction | ||||||
| Number of sequences | 79,681 | 95,970 | 74,740 | 74,498 | 77,535 | 74,317 |
| Sequences/Mb | 121.6 | 147.2 | 115.7 | 115.5 | 118.7 | 115.3 |
| Total length (contigs, Mb) | 654.6 | 651.6 (99,5%*) | 645.9 (98,6%*) | 644.7 (98,4%*) | 652.8 (99,7%*) | 644.3 (98,4%*) |
| Total length (scaffold, Mb) | 724.7 | 721.9 (99,6%*) | 714.6 (98,6%*) | 713.1 (98,4%*) | 722.9 (99,7%*) | 712.3 (98,3%*) |
| L50 (Kb) | 17.5 | 13.5 | 8.9 | 8.9 | 9.5 | 8.9 |
| N50 | 10,596 | 13,964 | 20,425 | 20,491 | 19,621 | 20,504 |
| L90 (Kb) | 3,4 | 1,3 | 1,3 | 1,3 | 1,4 | 1,4 |
| N90 | 41,711 | 46,781 | 46,036 | 45,970 | 45,776 | 45,799 |
| G + C % | 32.00% | 35.18% | 35.04% | 35.08% | 35.28% | 35.01% |
| N° of sequences > 10 Kb | 20,561 | 20,897 | 19,975 | 19,915 | 20,454 | 19,922 |
| Number of genes | 28,310 | 27,785 | 27,121 | 27,160 | 28,029 | 27,326 |
| Number of proteins with IPR | 22,571 (79.7%) | 22,199 (79.9%) | 21,898 (80.7%) | 21,888 (80.6%) | 22,406 (80%) | 21,997 (80.5%) |
Sequencing (Illumina), assembly (ABySS-based91), genome reconstruction (IMR/DENOM41) and gene prediction statistics of the A41, VS, VT, C3 and SP genotypes. The reference genome (2 C) data of the libraries are available in Scaglione et al.23. *Percentage of reconstructed genome compared with the 2 C genome.