# Quercus robur Genome data
############################

# Genome assemblies
#-------------------
# haploid version, 12 pseudo chromosomes + 538 unassigned scaffold
Qrob_PM1N.fa
#JBrowse:    https://urgi.versailles.inra.fr/WebApollo_oak_PM1N/jbrowse
#Intermine:  https://urgi.versailles.inra.fr/OakMine_PM1N/begin.do

# diploid version 2, 8827 scaffolds
Qrob_V2_2N.fa
#JBrowse:    https://urgi.versailles.inra.fr/WebApollo_oak_V2/jbrowse

# diploid version 1, 8827 scaffolds, 17910 scaffolds, Plomion et al, 2015
Qrob_V1_2N.fa

#Genes
#-----

#Quercus robur CDS (aa) predicted on PM1N (Haploid Version)
Qrob_PM1N_CDS_aa_20161004.fa

#Quercus robur CDS (nt) predicted on PM1N (Haploid Version)
Qrob_PM1N_CDS_nt_20161004.fa

#Oak transcriptome
#-------------------

#Oak transcriptome (de novo assembly ; Lesur et al. 2015)
OCV4_assembly_final.fsa

#Oak genome annotation files (GFF format)
#-----------------------------------------

#Quercus robur genes annotated on PM1N (Haploid Version)
Qrob_PM1N_genes_20161004.gff.gz

#Quercus robur Transposable elements annotated on PM1N (Haploid Version)
Qrob_PM1N_refTEs.gff.gz

#Quercus robur genes annotated on PM1N (Haploid Version)- All 43755 genes before filtering
Qrob_PM1N_genes_20151214_43755.gff.zip

	1177 "gene_qual=manual" #genes manually curated
	28488 "gene_qual=regular" # [N<20%] AND [[length > 500 nt] OR [length < 500 nt AND oak transcript evidence > 90%]]
	515 "gene_qual=uncomplete" # [without start or/and stop] OR [N>20%]
	13575 " "gene_qual=unreliable" #"low confidence" genes with length < 500 nt without transcript evidence > 90% of coverage