Table 4 Polymorphism detection in the tetraploid wheat assembly and polymorphism phasing
From: Separating homeologs by phasing in the tetraploid wheat transcriptome
Polymorphisms before phasing | Â |
|---|---|
Polymorphisms (n) | 1,179,465 |
Singlenucleotide polymorphisms (SNP) (n) | 958,362 |
Multi-nucleotide polymorphisms (MNP) (n) | 23,424 |
Insertions | 72,144 |
Deletions | 39,882 |
Complexa | 84,457 |
Other (>2 alleles)b | 1,089 |
Phasing (HapCUT) | Â |
Contigs with <2 SNP/MNP (n) | 65,238 |
Contigs with >1 SNP/MNP (n) | 74,880 |
Phased contigs (n) | 67,169 |
Phased blocks (n) | 81,413 |
Phased SNPs/MNPs (n) | 864,865 |
Chimeric reference contigs (n) | 34,029 |
Readphaser | Â |
Reads filtered due to mapping quality <30 (n) | 106,003,190 |
Reads filtered due to indels (n) | 6,544,331 |
Reads passed to MIRA (n) | 256,016,046 |