Reads were mapped to Human GRCh38 (GCA_000001405.15) with dbSNP150 and Ensembl 90 annotation using HISAT249, and annotated against dbSNP150 and Ensembl 90.
Variants were annotated against the UCSC KnownGene annotation, dbSNP132, and the May 2011 release of the 1000 Genomes Project using ANNOVAR.
All the transcripts were annotated against V1 of the 12X draft annotation of the grapevine genome allowing ~80% of the modulated genes to be identified (Additional file 2).
Due to limited annotation of Rhesus Monkey genome, the microarray probes are annotated against human genes and ontology.
Wild-type and mutant genes were annotated against the v1 version of the 12x draft annotation of the grapevine genome using the CRIBI tools [ 42] combined with the grapevine molecular network VitisNet [ 43].
All the transcripts were annotated against the V1 version of the 12X draft annotation of the grapevine genome http://genomes.cribi.unipd.it/DATA/ allowing 70% of the modulated genes to be identified (Additional File 2).
Not surprisingly, only 367 (59%) of these could not be annotated against UniProt, which is lower than the transcripts aligning in annotated regions (88%, p < 10-16, Fisher's exact test).
In total, 38,215 unigenes were annotated against the Swiss-Prot database, accounting for 62.94% of all annotated unigenes and 246 unigenes that were not annotated against the other three databases (Additional file 6: Figure S3A).
Total proteins from each of the 15 metagenomes were first annotated against the KEGG functional database79 using the KEGG Automatic Annotation Server80.
In order to further prioritize SNPs with potential functional effects, the sets were functionally annotated against gene transcripts and ENCODE features.
De novo assembly resulted in 48,783 good quality transcripts, of which 67% of transcripts could be annotated against NCBI non – redundant database.
