Mapping by sequencing of son1
Genomic DNA was extracted from 20 day old plants using the Quiagen plant maxi kit and eluted into 1 ml of AE elution buffer. DNA was quantified using a nanodrop. Sequencing libraries were prepared using Ilumina Tru-seq. DNA was sequenced by VIB nucleomics (Ghent, Belgium) using an Ilummina Hi-seq 2000. Paired-end reads supplied in fastq format were trimmed using Fast X0.0.13 to remove reads with Q<20 or read length <35bp. Adapters were removed using cutadapt 1.2.1. Reads were further filtered to remove reads with greater than 90% A content (poly-A reads), all ambiguous reads containing an N in any position, reads with <Q25 and artefact reads using FastX 0.0.13 and ShortRead 1.20.0. Contaminant reads were removed by discarding reads which aligned to phix_illumina using Bowtie 2.1.0.