Release 3.1.1

This release addresses an inconsistencies and incompleteness of the rRNA annotation specific to the CHM13 version of the CHESS annotation.

Changelog

1. rRNA annotation moved over from the official RefSeq CHM13 annotation, including all annotated copies
2. New gene and transcript IDs were assigned consistent with the CHS nomenclature
3. rRNA1 and rRNA2 genes on chrM assigned matching CHSID for GRCh38 and CHM13

Statement

Chess Release 3.1.1

Files

Filenames	Genome	Content	Description
chess3.1.1.GRCh38.gff.gz, chess3.1.1.GRCh38.gtf.gz, chess3.1.1.GRCh38.bb.gz	GRCh38	CHESS gene annotation	This file contains the primary gene set described in the CHESS paper. All genes and transcripts are mapped onto human genome release GRCh38.p12. Included in this file are genes on the reference chromosomes, unmapped scaffolds, assembly patches, and alternate loci.
chess3.1.1.CHM13.gff.gz, chess3.1.1.CHM13.gtf.gz, chess3.1.1.CHM13.bb.gz	CHM13	CHESS gene annotation on CHM13	This file contains the primary gene set described in the CHESS paper mapped over to the CHM13 human reference genome.
chess3.1.1.GRCh38.primary.gff.gz, chess3.1.1.GRCh38.primary.gtf.gz	GRCh38	CHESS gene annotation excluding alternative scaffolds	This file contains the primary gene set described in the CHESS paper but excludes annotations of any alternative scaffolds. All genes and transcripts are mapped onto human genome release GRCh38.p12.
chess3.1.1.GRCh38.protein.fa.gz	GRCh38	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes based on the GRCh38 human reference genome.
chess3.1.1.CHM13.protein.fa.gz	CHM13	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes based on the CHM13 human reference genome.
chess3.1.1.mapfile.tsv	-	Cross-Reference	This tab-separated file contains a list of transcript identifiers in CHESS 3.1.0 along with the corresponding identifiers in other popular databases (RefSeq, GENCODE, CHESS2) .
assembled.gtf.gz	GRCh38	Assembled Transcripts	Noise-filtered set of assembled GTEx transcripts used to generate the final CHESS dataset.

Summary

	genes	transcripts
protein_coding	19838	99201
lncRNA	17624	34709
pseudogene	16774	17263
other	4269	7190
alt_scaffolds	5250	10088