Table 4

Polymorphism detection in the tetraploid wheat assembly and polymorphism phasing

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


aComplex: composite insertions and substitution events.

bOther: includes cases with >1 alternative allele.

Krasileva et al. Genome Biology 2013 14:R66   doi:10.1186/gb-2013-14-6-r66

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