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Figure 3 | Genome Medicine

Figure 3

From: BAIT: Organizing genomes and mapping rearrangements in single cells

Figure 3

Clustering contigs into linkage groups for early-assembly genomes. Using template strand directionality as a unique signature, all contigs in the early mouse assembly MGSCv3 were compared with each other across all 62 Strand-seq libraries. All contigs with similar (>85%) template inheritance patterns were stratified into linkage groups (LGs). (a) Heat plots of all BAIT-called LGs show limited similarity between groups. Through analysis of homozygous template states only (WW and CC, left panel) 57,581 contigs cluster into 33 LGs, with the association between linkage groups appearing as yellow points if groups are in the same orientation, or blue points if the groups are in opposite orientations. The LGs are then reanalyzed after merging and reorientation of associated clusters, resulting in only 20 linkage groups consisting of 54,832 contigs. (b) Histogram of the number of fragments within a linkage group that map to a particular chromosome. The LG with the largest number of contigs are shown at the bottom in dark gray, with groups that contain the next largest numbers of contigs shown in progressively lighter grays. Most LGs contain contigs that belong to the same chromosome (see Additional file 4: Figure S3), and in general, most chromosomes are represented by one or two linkage groups. Note: contigs derived from sex chromosomes in male libraries can be distinguished as they are haploid, and are not computed as an initial heat plot. Any contigs derived from haploid chromosomes are separated and clustered independently. Almost all contigs clustered into this linkage group mapped to the X chromosome (right histogram). Abbreviations: C, Crick; W, Watson.

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