Identification of SNPs for generation of SBP markers in Arabidopsis thaliana. (a) SHORE analysis of a 2.95 Kb DNA fragment of the lower arm of chromosome V between 25,034,700 and 25,037,650 bps resulted in four SNPs. Name, name of the project; Position, position within the chromosome; Ref base, nucleotide of the sequenced genome (Col-0); Cons base, Consensus base (Nd-0); Read type, part of the reads used for prediction were non-repetitive; Support, number of reads supporting a predicted feature; Concordance: Ratio of reads to total coverage of the sequenced genome. Max Quality, highest base quality supporting a prediction; Avg hits, average number of alignments of all reads covering this genomic position. (b) Two SNPs at positions 25,037,599 and 25,037,602 nucleotides [in bold font in (a)] were aligned in three Nd-0 Solexa reads with staggered ends. (c) Three 75 bp Nd-0 Solexa reads were aligned with the reference genome Col-0 (Query Sequence). Two SNPs were circled. Note that the three reads were from three independent DNA molecules.
Sahu et al. BMC Genomics 2012 13:20 doi:10.1186/1471-2164-13-20