GFF Files with Feature Type Counts Generated on: Mon Oct 6 03:46:19 UTC 2025 ======================================== Each file is listed with counts for all feature types present. ======================================== File: ./D-Apul/data/Apulchra-genome.gff ---------------------------------------- CDS : 201613 exon : 209537 gene : 44371 mRNA : 36447 tRNA : 7924 ---------------------------------------- TOTAL FEATURES : 499892 ======================================== File: ./D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/Results.gff3 ---------------------------------------- MIRNA_hairpin : 51 Unknown_sRNA_locus : 18768 mature_miRNA : 51 miRNA-star : 51 siRNA21_locus : 8 siRNA22_locus : 21 siRNA23_locus : 25 siRNA24_locus : 12 ---------------------------------------- TOTAL FEATURES : 18987 ======================================== File: ./D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/known_miRNAs.gff3 ---------------------------------------- sRNA : 1613 ---------------------------------------- TOTAL FEATURES : 1613 ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apul.GFFannotation.3UTR_1kb.gff ---------------------------------------- 3prime_UTR : 36447 ---------------------------------------- TOTAL FEATURES : 36447 ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apul.GFFannotation.3UTR_1kb_corrected.gff ---------------------------------------- 3prime_UTR : 37359 ---------------------------------------- TOTAL FEATURES : 37359 ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apul.GFFannotation.5UTR_1kb.gff ---------------------------------------- five_prime_UTR : 36447 ---------------------------------------- TOTAL FEATURES : 36447 ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apul.GFFannotation.5UTR_1kb_corrected.gff ---------------------------------------- five_prime_UTR : 37158 ---------------------------------------- TOTAL FEATURES : 37158 ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apul_GFFannotation.mRNA_sorted.gff ---------------------------------------- mRNA : 36447 ---------------------------------------- TOTAL FEATURES : 36447 ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apulcra-genome-CDS_only.gff ---------------------------------------- CDS : 201613 ---------------------------------------- TOTAL FEATURES : 201613 ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apulcra-genome-mRNA_only.gff ---------------------------------------- mRNA : 36447 ---------------------------------------- TOTAL FEATURES : 36447 ======================================== File: ./D-Apul/output/06-Apul-miRNA-mRNA-RNAhybrid/Apul-RNAhybrid-3UTR-compact_3utr_worm.gff ---------------------------------------- miRNA_binding : 1041 ---------------------------------------- TOTAL FEATURES : 1041 ======================================== File: ./D-Apul/output/06-Apul-miRNA-mRNA-RNAhybrid/Apul-RNAhybrid-5UTR-compact_3utr_worm.gff ---------------------------------------- miRNA_binding : 1191 ---------------------------------------- TOTAL FEATURES : 1191 ======================================== File: ./D-Apul/output/06-Apul-miRNA-mRNA-RNAhybrid/Apul-RNAhybrid-mRNA-compact_3utr_worm.gff ---------------------------------------- miRNA_binding : 6559 ---------------------------------------- TOTAL FEATURES : 6559 ======================================== File: ./D-Apul/output/06-Apul-miRNA-mRNA-RNAhybrid/Apulcra-genome-mRNA_only_MAX1000.gff ---------------------------------------- mRNA : 232746 ---------------------------------------- TOTAL FEATURES : 232746 ======================================== File: ./D-Apul/output/06-Apul-miRNA-mRNA-RNAhybrid/Apulcra-genome-mRNA_only_MAX1000_formatted.gff ---------------------------------------- mRNA : 232746 ---------------------------------------- TOTAL FEATURES : 232746 ======================================== File: ./D-Apul/output/28-Apul-CpG-Annotation/CDS.gff ---------------------------------------- CDS : 201613 ---------------------------------------- TOTAL FEATURES : 201613 ======================================== File: ./D-Apul/output/28-Apul-CpG-Annotation/CGoutput-10seq.gff ---------------------------------------- nucleotide_motif : 195480 ---------------------------------------- TOTAL FEATURES : 195480 ======================================== File: ./D-Apul/output/28-Apul-CpG-Annotation/exon.gff ---------------------------------------- exon : 209537 ---------------------------------------- TOTAL FEATURES : 209537 ======================================== File: ./D-Apul/output/28-Apul-CpG-Annotation/gene.gff ---------------------------------------- gene : 44371 ---------------------------------------- TOTAL FEATURES : 44371 ======================================== File: ./D-Apul/output/28-Apul-CpG-Annotation/tRNA.gff ---------------------------------------- tRNA : 7924 ---------------------------------------- TOTAL FEATURES : 7924 ======================================== File: ./E-Peve/data/Porites_evermanni_v1.annot.gff ---------------------------------------- CDS : 231320 UTR : 15098 mRNA : 40389 ---------------------------------------- TOTAL FEATURES : 286807 ======================================== File: ./E-Peve/data/Porites_evermanni_validated.gff3 ---------------------------------------- CDS : 231320 UTR : 15098 exon : 246418 gene : 40389 mRNA : 40389 ---------------------------------------- TOTAL FEATURES : 573614 ======================================== File: ./E-Peve/output/00.01-Peve-gene-gff/Peve_gene_only.gff3 ---------------------------------------- gene : 40389 ---------------------------------------- TOTAL FEATURES : 40389 ======================================== File: ./E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/Results.gff3 ---------------------------------------- MIRNA_hairpin : 48 Unknown_sRNA_locus : 15578 mature_miRNA : 48 miRNA-star : 48 siRNA21_locus : 16 siRNA22_locus : 18 siRNA23_locus : 25 siRNA24_locus : 18 ---------------------------------------- TOTAL FEATURES : 15799 ======================================== File: ./E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/known_miRNAs.gff3 ---------------------------------------- sRNA : 2562 ---------------------------------------- TOTAL FEATURES : 2562 ======================================== File: ./F-Ptua/data/Pocillopora_meandrina_HIv1.genes-validated.gff3 ---------------------------------------- CDS : 208535 exon : 208535 gene : 31840 mRNA : 31840 ---------------------------------------- TOTAL FEATURES : 480750 ======================================== File: ./F-Ptua/data/Pocillopora_meandrina_HIv1.genes.gff3 ---------------------------------------- CDS : 208535 exon : 208535 transcript : 31840 ---------------------------------------- TOTAL FEATURES : 448910 ======================================== File: ./F-Ptua/output/00.01-Ptua-gene-gff/Pmea_gene_only.gff3 ---------------------------------------- gene : 31840 ---------------------------------------- TOTAL FEATURES : 31840 ======================================== File: ./F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/Results.gff3 ---------------------------------------- MIRNA_hairpin : 40 Unknown_sRNA_locus : 7126 mature_miRNA : 40 miRNA-star : 40 siRNA21_locus : 13 siRNA22_locus : 16 siRNA23_locus : 19 siRNA24_locus : 7 ---------------------------------------- TOTAL FEATURES : 7301 ======================================== File: ./F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/known_miRNAs.gff3 ---------------------------------------- sRNA : 1856 ---------------------------------------- TOTAL FEATURES : 1856