Fig. 4

Sequence comparison of different assemblies. (a) Chromosome 4 of HapSK, hapB73 assembly (generated by gcaPDA) and reference B73 (B73) assembly were aligned to chromosome 4 of reference SK assembly (the alignments colored with green, blue and purple, respectively). Inset at upper left: a large inversion (c. 8 Mb) between B73 and SK. Inset at lower right: a large InDel (c. 3 Mb) between B73 and SK. (b) Sequence alignments of the ZmBAM1d locus, which is known as highly divergent between B73 and SK. Numbers with circles indicate large InDels between SK and B73. Coverage and identity of the alignments are shown on the left. ZmBAM1d genes is represented as a green brick