GFF/GFF3 File Detailed Analysis Generated on: Mon Oct 6 03:45:42 UTC 2025 ======================================== ======================================== File: ./D-Apul/data/Apulchra-genome.gff ---------------------------------------- Size: 46548210 bytes Total Lines: 499893 Feature Lines: 499892 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 1 Feature Types: - CDS - exon - gene - mRNA - tRNA Feature Type Counts: CDS: 201613 exon: 209537 gene: 44371 mRNA: 36447 tRNA: 7924 Has GFF3 header (##gff-version 3): Yes Sample Attributes (from first 3 feature lines): ID=FUN_000001; ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein; ID=FUN_000001-T1.exon1;Parent=FUN_000001-T1; Sources: funannotate ======================================== File: ./D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/Results.gff3 ---------------------------------------- Size: 1948206 bytes Total Lines: 18987 Feature Lines: 18987 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - MIRNA_hairpin - Unknown_sRNA_locus - mature_miRNA - miRNA-star - siRNA21_locus - siRNA22_locus - siRNA23_locus - siRNA24_locus Feature Type Counts: 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 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=Cluster_1;DicerCall=N;MIRNA=N ID=Cluster_2;DicerCall=N;MIRNA=N ID=Cluster_3;DicerCall=N;MIRNA=N Sources: ShortStack ======================================== File: ./D-Apul/output/04-Apul-sRNA-discovery-ShortStack/ShortStack_out/known_miRNAs.gff3 ---------------------------------------- Size: 113111 bytes Total Lines: 1613 Feature Lines: 1613 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 1 Feature Types: - sRNA Feature Type Counts: sRNA: 1613 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=bfl-miR-153 ID=mmu-miR-7238-3p ID=dme-miR-2491-3p Sources: ShortStack ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apul.GFFannotation.3UTR_1kb.gff ---------------------------------------- Size: 4093535 bytes Total Lines: 36447 Feature Lines: 36447 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - 3prime_UTR Feature Type Counts: 3prime_UTR: 36447 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=FUN_002303-T1;Parent=FUN_002303;product=hypothetical ID=FUN_002304-T1;Parent=FUN_002304;product=hypothetical ID=FUN_002305-T1;Parent=FUN_002305;product=hypothetical Sources: funannotate ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apul.GFFannotation.3UTR_1kb_corrected.gff ---------------------------------------- Size: 4195984 bytes Total Lines: 37359 Feature Lines: 37359 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - 3prime_UTR Feature Type Counts: 3prime_UTR: 37359 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=FUN_002303-T1;Parent=FUN_002303;product=hypothetical ID=FUN_002304-T1;Parent=FUN_002304;product=hypothetical ID=FUN_002305-T1;Parent=FUN_002305;product=hypothetical Sources: funannotate ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apul.GFFannotation.5UTR_1kb.gff ---------------------------------------- Size: 4239367 bytes Total Lines: 36447 Feature Lines: 36447 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - five_prime_UTR Feature Type Counts: five_prime_UTR: 36447 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=FUN_002303-T1;Parent=FUN_002303;product=hypothetical ID=FUN_002304-T1;Parent=FUN_002304;product=hypothetical ID=FUN_002305-T1;Parent=FUN_002305;product=hypothetical Sources: funannotate ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apul.GFFannotation.5UTR_1kb_corrected.gff ---------------------------------------- Size: 4322206 bytes Total Lines: 37158 Feature Lines: 37158 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - five_prime_UTR Feature Type Counts: five_prime_UTR: 37158 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=FUN_002303-T1;Parent=FUN_002303;product=hypothetical ID=FUN_002304-T1;Parent=FUN_002304;product=hypothetical ID=FUN_002305-T1;Parent=FUN_002305;product=hypothetical Sources: funannotate ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apul_GFFannotation.mRNA_sorted.gff ---------------------------------------- Size: 4202931 bytes Total Lines: 36447 Feature Lines: 36447 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - mRNA Feature Type Counts: mRNA: 36447 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=FUN_002303-T1;Parent=FUN_002303;product=hypothetical protein; ID=FUN_002304-T1;Parent=FUN_002304;product=hypothetical protein; ID=FUN_002305-T1;Parent=FUN_002305;product=hypothetical protein; Sources: funannotate ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apulcra-genome-CDS_only.gff ---------------------------------------- Size: 18605231 bytes Total Lines: 201613 Feature Lines: 201613 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 2 Feature Types: - CDS Feature Type Counts: CDS: 201613 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=FUN_000001-T1.cds;Parent=FUN_000001-T1; ID=FUN_000001-T1.cds;Parent=FUN_000001-T1; ID=FUN_000001-T1.cds;Parent=FUN_000001-T1; Sources: funannotate ======================================== File: ./D-Apul/output/05-Apul-annotate-UTRs/Apulcra-genome-mRNA_only.gff ---------------------------------------- Size: 4202931 bytes Total Lines: 36447 Feature Lines: 36447 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - mRNA Feature Type Counts: mRNA: 36447 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein; ID=FUN_000002-T1;Parent=FUN_000002;product=hypothetical protein; ID=FUN_000003-T1;Parent=FUN_000003;product=hypothetical protein; Sources: funannotate ======================================== File: ./D-Apul/output/06-Apul-miRNA-mRNA-RNAhybrid/Apul-RNAhybrid-3UTR-compact_3utr_worm.gff ---------------------------------------- Size: 141036 bytes Total Lines: 1042 Feature Lines: 1041 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - miRNA_binding Feature Type Counts: miRNA_binding: 1041 Has GFF3 header (##gff-version 3): Yes Sample Attributes (from first 3 feature lines): ID=Cluster_1832.mature::ntLink_6:4847465-4847486(-);MFE=-27.8;Pval=0.036639 ID=Cluster_1832.mature::ntLink_6:4847465-4847486(-);MFE=-26.7;Pval=0.014807 ID=Cluster_1832.mature::ntLink_6:4847465-4847486(-);MFE=-27.7;Pval=0.038633 Sources: RNAhybrid ======================================== File: ./D-Apul/output/06-Apul-miRNA-mRNA-RNAhybrid/Apul-RNAhybrid-5UTR-compact_3utr_worm.gff ---------------------------------------- Size: 161434 bytes Total Lines: 1192 Feature Lines: 1191 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - miRNA_binding Feature Type Counts: miRNA_binding: 1191 Has GFF3 header (##gff-version 3): Yes Sample Attributes (from first 3 feature lines): ID=Cluster_1832.mature::ntLink_6:4847465-4847486(-);MFE=-33.3;Pval=0.001912 ID=Cluster_1832.mature::ntLink_6:4847465-4847486(-);MFE=-26.7;Pval=0.014807 ID=Cluster_1832.mature::ntLink_6:4847465-4847486(-);MFE=-27.4;Pval=0.045273 Sources: RNAhybrid ======================================== File: ./D-Apul/output/06-Apul-miRNA-mRNA-RNAhybrid/Apul-RNAhybrid-mRNA-compact_3utr_worm.gff ---------------------------------------- Size: 888083 bytes Total Lines: 6560 Feature Lines: 6559 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - miRNA_binding Feature Type Counts: miRNA_binding: 6559 Has GFF3 header (##gff-version 3): Yes Sample Attributes (from first 3 feature lines): ID=Cluster_1819.mature::ntLink_6:4140247-4140268(+);MFE=-25.5;Pval=0.024765 ID=Cluster_1819.mature::ntLink_6:4140247-4140268(+);MFE=-20.6;Pval=0.047103 ID=Cluster_1819.mature::ntLink_6:4140247-4140268(+);MFE=-27.2;Pval=0.020408 Sources: RNAhybrid ======================================== File: ./D-Apul/output/06-Apul-miRNA-mRNA-RNAhybrid/Apulcra-genome-mRNA_only_MAX1000.gff ---------------------------------------- Size: 26840588 bytes Total Lines: 232746 Feature Lines: 232746 GFF3 Compliant (9 fields): No Field counts found: 10 9 Attribute count (first line): 3 Feature Types: - mRNA Feature Type Counts: mRNA: 232746 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical Sources: funannotate ======================================== File: ./D-Apul/output/06-Apul-miRNA-mRNA-RNAhybrid/Apulcra-genome-mRNA_only_MAX1000_formatted.gff ---------------------------------------- Size: 26840588 bytes Total Lines: 232746 Feature Lines: 232746 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - mRNA Feature Type Counts: mRNA: 232746 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein; ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein; ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein; Sources: funannotate ======================================== File: ./D-Apul/output/28-Apul-CpG-Annotation/CDS.gff ---------------------------------------- Size: 18605247 bytes Total Lines: 201614 Feature Lines: 201613 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 2 Feature Types: - CDS Feature Type Counts: CDS: 201613 Has GFF3 header (##gff-version 3): Yes Sample Attributes (from first 3 feature lines): ID=FUN_000001-T1.cds;Parent=FUN_000001-T1; ID=FUN_000001-T1.cds;Parent=FUN_000001-T1; ID=FUN_000001-T1.cds;Parent=FUN_000001-T1; Sources: funannotate ======================================== File: ./D-Apul/output/28-Apul-CpG-Annotation/CGoutput-10seq.gff ---------------------------------------- Size: 19286789 bytes Total Lines: 195530 Feature Lines: 195480 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 2 Feature Types: - nucleotide_motif Feature Type Counts: nucleotide_motif: 195480 Has GFF3 header (##gff-version 3): Yes Sample Attributes (from first 3 feature lines): ID=ptg000048l.1;note=*pat pattern:CG ID=ptg000048l.2;note=*pat pattern:CG ID=ptg000048l.3;note=*pat pattern:CG Sources: fuzznuc ======================================== File: ./D-Apul/output/28-Apul-CpG-Annotation/exon.gff ---------------------------------------- Size: 20020898 bytes Total Lines: 209538 Feature Lines: 209537 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 2 Feature Types: - exon Feature Type Counts: exon: 209537 Has GFF3 header (##gff-version 3): Yes Sample Attributes (from first 3 feature lines): ID=FUN_000001-T1.exon1;Parent=FUN_000001-T1; ID=FUN_000001-T1.exon2;Parent=FUN_000001-T1; ID=FUN_000001-T1.exon3;Parent=FUN_000001-T1; Sources: funannotate ======================================== File: ./D-Apul/output/28-Apul-CpG-Annotation/gene.gff ---------------------------------------- Size: 2899257 bytes Total Lines: 44372 Feature Lines: 44371 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 1 Feature Types: - gene Feature Type Counts: gene: 44371 Has GFF3 header (##gff-version 3): Yes Sample Attributes (from first 3 feature lines): ID=FUN_000001; ID=FUN_000002; ID=FUN_000003; Sources: funannotate ======================================== File: ./D-Apul/output/28-Apul-CpG-Annotation/tRNA.gff ---------------------------------------- Size: 819925 bytes Total Lines: 7925 Feature Lines: 7924 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - tRNA Feature Type Counts: tRNA: 7924 Has GFF3 header (##gff-version 3): Yes Sample Attributes (from first 3 feature lines): ID=FUN_000214-T1;Parent=FUN_000214;product=tRNA-Ala; ID=FUN_000218-T1;Parent=FUN_000218;product=tRNA-Gly; ID=FUN_000241-T1;Parent=FUN_000241;product=tRNA-Thr; Sources: funannotate ======================================== File: ./E-Peve/data/Porites_evermanni_v1.annot.gff ---------------------------------------- Size: 24867416 bytes Total Lines: 286807 Feature Lines: 286807 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 5 Feature Types: - CDS - UTR - mRNA Feature Type Counts: CDS: 231320 UTR: 15098 mRNA: 40389 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=Peve_00000001;Name=Peve_00000001;start=0;stop=1;cds_size=543 Parent=Peve_00000001 Parent=Peve_00000001 Sources: Gmove ======================================== File: ./E-Peve/data/Porites_evermanni_validated.gff3 ---------------------------------------- Size: 55138300 bytes Total Lines: 620134 Feature Lines: 573614 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 1 Feature Types: - CDS - UTR - exon - gene - mRNA Feature Type Counts: CDS: 231320 UTR: 15098 exon: 246418 gene: 40389 mRNA: 40389 Has GFF3 header (##gff-version 3): Yes Sample Attributes (from first 3 feature lines): ID=gene-Peve_00000001 ID=mrna-00001;Parent=gene-Peve_00000001;Name=Peve_00000001;start=0;stop=1;cds_size=543 ID=cds-00001;Parent=mrna-00001 Sources: Gmove ======================================== File: ./E-Peve/output/00.01-Peve-gene-gff/Peve_gene_only.gff3 ---------------------------------------- Size: 3304513 bytes Total Lines: 40389 Feature Lines: 40389 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 1 Feature Types: - gene Feature Type Counts: gene: 40389 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=gene-Peve_00000001 ID=gene-Peve_00000039 ID=gene-Peve_00000112 Sources: Gmove ======================================== File: ./E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/Results.gff3 ---------------------------------------- Size: 1864930 bytes Total Lines: 15799 Feature Lines: 15799 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - MIRNA_hairpin - Unknown_sRNA_locus - mature_miRNA - miRNA-star - siRNA21_locus - siRNA22_locus - siRNA23_locus - siRNA24_locus Feature Type Counts: 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 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=Cluster_1;DicerCall=N;MIRNA=N ID=Cluster_2;DicerCall=N;MIRNA=N ID=Cluster_3;DicerCall=N;MIRNA=N Sources: ShortStack ======================================== File: ./E-Peve/output/08-Peve-sRNA-discovery-ShortStack/ShortStack_out/known_miRNAs.gff3 ---------------------------------------- Size: 217065 bytes Total Lines: 2562 Feature Lines: 2562 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 1 Feature Types: - sRNA Feature Type Counts: sRNA: 2562 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=mmu-miR-466i-5p ID=mmu-miR-466i-5p ID=mmu-miR-466i-5p Sources: ShortStack ======================================== File: ./F-Ptua/data/Pocillopora_meandrina_HIv1.genes-validated.gff3 ---------------------------------------- Size: 87247609 bytes Total Lines: 512785 Feature Lines: 480750 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 1 Feature Types: - CDS - exon - gene - mRNA Feature Type Counts: CDS: 208535 exon: 208535 gene: 31840 mRNA: 31840 Has GFF3 header (##gff-version 3): Yes Sample Attributes (from first 3 feature lines): ID=gene-Pocillopora_meandrina_HIv1___RNAseq.g29951.t1 ID=mrna-Pocillopora_meandrina_HIv1___RNAseq.g29951.t1;Parent=gene-Pocillopora_meandrina_HIv1___RNAseq.g29951.t1 ID=cds-Pocillopora_meandrina_HIv1___RNAseq.g29951.t1;Parent=mrna-Pocillopora_meandrina_HIv1___RNAseq.g29951.t1 Sources: AUGUSTUS ======================================== File: ./F-Ptua/data/Pocillopora_meandrina_HIv1.genes.gff3 ---------------------------------------- Size: 56828984 bytes Total Lines: 448910 Feature Lines: 448910 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 1 Feature Types: - CDS - exon - transcript Feature Type Counts: CDS: 208535 exon: 208535 transcript: 31840 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=Pocillopora_meandrina_HIv1___TS.g23774.t1 Parent=Pocillopora_meandrina_HIv1___TS.g23774.t1 Parent=Pocillopora_meandrina_HIv1___TS.g23774.t1 Sources: AUGUSTUS ======================================== File: ./F-Ptua/output/00.01-Ptua-gene-gff/Pmea_gene_only.gff3 ---------------------------------------- Size: 4073475 bytes Total Lines: 31840 Feature Lines: 31840 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 1 Feature Types: - gene Feature Type Counts: gene: 31840 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=gene-Pocillopora_meandrina_HIv1___RNAseq.g29951.t1 ID=gene-Pocillopora_meandrina_HIv1___RNAseq.g29952.t1 ID=gene-Pocillopora_meandrina_HIv1___RNAseq.g29953.t1 Sources: AUGUSTUS ======================================== File: ./F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/Results.gff3 ---------------------------------------- Size: 945693 bytes Total Lines: 7301 Feature Lines: 7301 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 3 Feature Types: - MIRNA_hairpin - Unknown_sRNA_locus - mature_miRNA - miRNA-star - siRNA21_locus - siRNA22_locus - siRNA23_locus - siRNA24_locus Feature Type Counts: 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 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=Cluster_1;DicerCall=N;MIRNA=N ID=Cluster_2;DicerCall=N;MIRNA=N ID=Cluster_3;DicerCall=N;MIRNA=N Sources: ShortStack ======================================== File: ./F-Ptua/output/04-Ptua-sRNA-discovery-ShortStack/ShortStack_out/known_miRNAs.gff3 ---------------------------------------- Size: 183707 bytes Total Lines: 1856 Feature Lines: 1856 GFF3 Compliant (9 fields): Yes Field counts found: 9 Attribute count (first line): 1 Feature Types: - sRNA Feature Type Counts: sRNA: 1856 Has GFF3 header (##gff-version 3): No Sample Attributes (from first 3 feature lines): ID=apa-mir-2050_Exaiptasia_pallida_Baumgarten_et_al._2017_miR-2050;_Nve;_Spis;_Adi ID=mmu-miR-466i-5p ID=mmu-miR-466i-5p Sources: ShortStack