Figure 4.

Alignment of a manually assembled contig from Ler-0, chr3:16.65–17.02 Mb to the reference annotated with SV-QTL. Thick black lines show alignments to reference genome. Blue arrows show the sources of cis SV-QTL; stacked arrows mean multiple read anomaly traits had SV-QTL. Red arrows display trans QTL with arrows starting from the source, and pointing toward the sink. Gaps in the contig alignment indicate loci where Ler-0 did not align to the reference, with the exception of two transposed segments that mapped to chromosomes 2 and 4 at positions concordant with the sources of two trans SV-QTL (circled).