# Reference genome * This genome is mapped to assembly BCM-After-Atlas (https://doi.org/10.15482/USDA.ADC/1173238) # File description for the release of OGSv1.2 original * .gff - gff file of official gene set * transcript.fa - transcripts of all types of RNAs * cds.fa - cds sequences of mRNA * peptide.fa - peptide sequences of mRNA * IDmapping.csv - ID mapping table between OGSv1.2 and OGSv1.1 * statistics.csv - Statistics along with merging procedure #Changes in OGSv1.2 by K. Panfilio and I. Vargas-Jentzsch ## updates to 337 gene models ## 122 new gene models ## 9 gene models deleted ## All models lacking start and/or stop codons have been reviewed: all of these are partial or split models, and are indicated as such in the transcript name and/or in the comments sections. ## Conversely, models labeled as "-partial" but that have both the start and stop codon were verified: they are partial because internal exons are missing. # Quality control for manual curations from Web Apollo ## Automated correction for the following errors: * Models that do not share coding regions, but were wrongly formatted as isoforms (9 models) # Quality control for OGSv1.1 ## Automated correction for the following errors: * Redundant length of the gene (2 models) * A child feature over a coordinate boundary of its related gene (2 models) # OGS construction by integrating the models of manual curations from Web Apollo and OGSv1.1 OGSv1.1 models were replaced by the models of manual curations from Web Apollo according to 'replace' attributes. Newly added models were assigned with new unique IDs. Merged models and split models were also assigned with new unique IDs, while the corresponding old IDs were retired. Models with simple replacement would inherit the original IDs. Please see 'IDmapping.csv' for more details. # Post-processing of sequence modification ## peptide sequences amended because of stop_codon_read_through * OFAS025232-PA: readthrough stop codon required (translated as 'X') * OFAS025210-PA: readthrough stop codon required (translated as 'U') * OFAS027087-PA: readthrough stop codon required (translated as 'U') ## The gff of locus OFAS027004 was modified