Jbrowse Track Descriptions - Version 3 Annotation

Gene Annotation

• Representative HC Gene Models - Isoform with the longest CDS for each locus with a high confidence gene model
• HC Gene Models - High confidence gene models
• Working Gene Models - High confidence gene models and low confidence gene models (e.g. gene predictions with insufficient evidence, partial gene models, TE-related gene models, etc)

RNA-Seq Coverage

• RNA-seq reads aligned to the v3 genome assemblies with TopHat2.

Misc Annotation

• RepeatMasker - putative repeats identified by RepeatMasker (v4.0.5) using a species-specific repeat library

Reference Sequence

• Sequence of version 3 of the genome assembly (pseudomolecules)

Variant Calls

• SNPs indentified from WGS and RNA-seq read alignments