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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  
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)  
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  
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
  1. aComplex: composite insertions and substitution events.
  2. bOther: includes cases with >1 alternative allele.