Ursus americanus (Black Bear)

Visual overview of genome assembly metrics

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K-mer frequencies from the adapter-trimmed PacBio HiFi data used to estimate genome size, sequencing error rate, and heterozygosity. The main peak at ~37× coverage corresponds to homozygous regions of the genome, while the slight peak at ~18× corresponds to heterozygous regions of the genome. The peak around zero corresponds to probable sequencing errors.

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BlobToolKit Snail plot showing a graphical representation of the quality metrics for the primary assembly. The plot circle represents the full size of the assembly. From the inside-out, the central plot covers length-related metrics. The red line represents the size of the longest scaffold; all other scaffolds are arranged in size-order moving clockwise around the plot and drawn in grey starting from the outside of the central plot. Dark and light orange arcs show the scaffold N50 and scaffold N90 values. The central light grey spiral shows the cumulative scaffold count with a white line at each order of magnitude. White regions in this area reflect the proportion of Ns in the assembly The dark vs. light blue area around it shows mean, maximum and minimum GC vs. AT content at 0.1% intervals (Challis et al. 2020)

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Omni-C contact map for the primary assembly after manual curation shows the 3D organization of the genome, with darker areas indicating closer proximity. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between two of such regions. Scaffolds are separated by black lines and higher density corresponds to higher levels of fragmentation.

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Authors

Megan A. Supple, Merly Escalona, Jillian Adkins, Michael R. Buchalski, Nicolas Alexandre, Ruta M. Sahasrabudhe, Oanh Nguyen, Samuel Sacco, Colin Fairbairn, Eric Beraut, William Seligmann, Richard E. Green, Erin Meredith, Beth Shapiro

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