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[…] ed as "reference type (R)". If ≥80% of the reads were discordant with the reference base, the site was classified as "non-reference type (N)". If there were two alleles with ≥40% read support, the site was classified as "allelic (A)". Since we have two data sets from NIAS and CSHL, the classifications of the three sets (NIAS, CSHL and NIAS + CSHL) were combined and reexamined to decide the genotype for each site (Additional file ): "reference type", "sequencing error (Additional file )", "alleles between individuals” (Additional file ), "alleles within individuals” (Additional file ), and "low depth". SNPs classified as allelic variations were annotated based on the RAP-DB gene models using SnpEff v. 3.1 (Cingolani et al. ) (Additional file )., The genome of the same NIAS individual used in the Illumina re-sequencing was sequenced using the Roche GS FLX platform. Low quality bases (<Q20) were trimmed by the same method as that for the Illumina reads. Repetitive sequences were detected in each read using RepeatMasker Open-3.0 ( with the MIPS Repeat Element Database (mips-REdat) version 4.3 (; Spannagl et al. ) and the Triticeae Repeat Sequence Database release 10 ( All preprocessed reads were aligned to the reference genome using Megablast (version 2.2.24) with the following options: -F 'm D' -U T -e 1e-10 (Zhang et al. )., The final, error-corrected pseudomolecules were virtually digested with SwaI and aligned against the rice optical map. A total of 144 major discordances were annotated in the current build of rice pseudomolecules (Additional file ). Among these discordances, there were 53 physical gaps, including 19 telomeric gaps. The sizes of the gaps range from 0.6 kb to 2.4 Mb, measured by adding up the sizes of the un-matched optical fragments at the gap locations. The discordances were grouped into 5 classes:, Class 1: Physical gaps in the pseudomolecule;, Class 2: Missed fragment or extra fragment: only the […]

Pipeline specifications

Software tools SnpEff, RepeatMasker, BLASTN
Organisms Oryza sativa, Oryza sativa Japonica Group