Fig. 6

IWGSC RefSeq v1.0 chromosome 7A 338 Mb to 388 Mb region. a Dotplot of 338 Mb to 388 Mb region against the 10 Mb between 358 Mb and 368 Mb and indicates two regions (blue boxes) that are speculated to be integral to the centromere structure and involved in in situ CENH3 protein-antibody binding (Additional file 8: Figure S6); the left box at ca. 349 Mb is suggested to have an incomplete genome assembly due to a breakdown in the assembly process as indicated in Fig. 5a (lower panel), since both the Gydle and Bionano maps have breaks in the 349 Mb region. b ChIP-seq CENH3 data (SRA accessions SRR1686799 and SRR1686800) aligned to the 338 Mb to 388 Mb region, counted in 10 Kb bins. c Raw CSS reads of 7AS (SRA accession SRR697723) aligned to the 338 Mb to 388 Mb region (see also Additional file 8: Figure S7). d Raw CSS reads of 7AL (SRA accession SRR697675) aligned to the 338 Mb to 388 Mb region (see also Additional file 8: Figure S7). The dotted blue box indicates a segment of the 7AL centromere that is duplicated as discussed in the text. Unique alignments are shown in blue in both c and d and show the clear boundaries of 7AS and 7AL telosomes as well as a deletion in the 7AL telosome. Reads with multiple mapped locations are shown in red (single location selected randomly) and indicate that the core CRW region is represented in the raw 7AS reads, although at lower levels than on 7AL. Counts in bins of 100 Kb