Table 1. Neem genome assembly statistics.
| Assembly parameters | Velvet assembly from Illumina reads | MIRA assembly from 454 reads | Hybrid assembly of Genotype 1 |
|---|---|---|---|
| Total high quality reads | 168,895,379 | 2,762,254 | – |
| k-mer | 45 | – | – |
| Assembled genome size (Mb) | 216 | 157 | 268 |
| Total number of contigs | 94,780 | 1,21,184 | 68,604 |
| N50 (bp) | 22,263 | 1,463 | 15,948 |
| Maximum contig length (bp) | 2,41,126 | 43,859 | 241,170 |
| Mininum contig length (bp) | 89 | 52 | 89 |
| % of bases in contigs ≥ 1,000 bp | 93.31 | 74.54 | 94.65 |
| Total repeat size in Mb (%) | 59.81 (27.41) | 48.84 (31.05) | 86.90 (32.44) |
| Number of predicted genes in Augustus | 27,556 | 41,169 | 40,130 |
| Number of predicted genes in GeneScan | 35,501 | 57,356 | 52,617 |
| Number of Genes clustered from GeneScan and Augustus | 37,161 | 61,901 | 48,032 |
| No of genes with >100 bp | 34,992 | 52,957 | 44,495 |
| Genes with RNA seq evidence | 27,087 | 43,383 | 32,278 |
| Non-TE genes | 19,547 | 41,373 | 29,050 |