Calling SV genotypes

The insertions and deletions identified above were assessed for segregation across our entire resequenced population. Alignment files generated during SNP calling above were filtered to remove split and soft-clipped reads. Importantly, reads aligning to multiple locations were left in to preserve contiguity. SV-associated genomic intervals in the Nipponbare reference with >98% bases covered by one or more reads were considered support for the Nipponbare allele. If the Nipponbare interval was <20 bp (as in a CarGold insertion) then we required that at least one read span the entire interval and 5 bp flanking both sides. bamtools/bedcov commands used are provided (bedCovCommandForSegIndels.sh).