Fig. 3

sd1 gene SNP-Seek result for TN1 and mapping of the CX162 reads. a Screenshot of the Genotype search result of the SNP-Seek database for the sd1 gene. The blank green space for the TN1 cultivar assay CX162 signifies the absence of genomic DNA in TN1 with respect to the Nipponbare reference genome. According to the alignment in Fig. 1, the deleted region in Nipponbare sd1 lies in between 38,382,762 and 38,383,144 of chromosome 1 and is consistent with the missing TN1 SNPs in SNP-Seek with respect to the Nipponbare reference genome starting at position 38,382,846 up to position 38,383,066. b Mapping coverage of the TN1 (assay CX162) 3 K RGP reads onto the sd1 gene region of the TN1 genome. The bam file was filtered to only get the properly paired reads with the proper distance. The gray color means that the read sequence is identical to the TN1 genome. The red asterisk is the approximate location of the start of the sd1 deletion with respect to the Nipponbare genome. c Closeup of the asterisk area in Fig. 4b. It has the coordinate 40,362,230 in TN1 chromosome 1. It corresponds to the extra nucleotide that made the sd1 deletion in TN1 and IR8 382-bp, instead of 383-bp. It is covered by 6 properly mapped paired-end reads with the correct distance. Gray color means the read sequence are homozygous to the TN1 genome