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added the Hc1 mitogenome annotation
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@conchoecia
conchoecia committed Apr 26, 2020
1 parent 35b2ae6 commit c5c3b39
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4 changes: 2 additions & 2 deletions annotation/make_release.sh
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#!/bin/bash
RELEASE=Hcv1a1d20200324
RELEASE=Hcv1a1d20200414
mkdir ${RELEASE}_release
find ./final_output/ -type f -name "*" -exec cp {} ${RELEASE}_release \;
rm ${RELEASE}_release/*vcf*
Expand Down Expand Up @@ -43,6 +43,6 @@ mv ${RELEASE}_release/h1_*.fasta.gz ${RELEASE}_release/partly_phased/
mv ${RELEASE}_release/h2_*.fasta.gz ${RELEASE}_release/partly_phased/

# add the relase notes
cat raw_files/release_template.md | sed 's/RELEASEPREFIX/${RELEASE}' > ${RELEASE}_release/README_${RELEASE}.md
cat raw_files/release_template.md | sed "s/RELEASEPREFIX/${RELEASE}/g" > ${RELEASE}_release/README_${RELEASE}.md

tar -czvf ${RELEASE}_release.tar.gz ${RELEASE}_release
38 changes: 38 additions & 0 deletions annotation/raw_files/Hc1_mito.gff3
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##sequence-region MN544300.1 1 12564
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1403702
MN544300.1 Genbank region 1 12564 . + . ID=MN544300.1:1..12564;Dbxref=taxon:1403702;Is_circular=true;Name=MT;gbkey=Src;genome=mitochondrion;isolate=Hc1;mol_type=genomic DNA;note=BioSample: SAMN12924379
MN544300.1 Genbank gene 1 1539 . + . ID=gene-COX1;Name=COX1;gbkey=Gene;gene=COX1;gene_biotype=protein_coding
MN544300.1 Genbank CDS 1 1539 . + 0 ID=cds-QIA92679.1;Parent=gene-COX1;Dbxref=NCBI_GP:QIA92679.1;Name=QIA92679.1;Note=COX1;gbkey=CDS;gene=COX1;product=cytochrome c oxidase subunit I;protein_id=QIA92679.1;transl_table=4
MN544300.1 Genbank gene 1544 1681 . + . ID=gene-URF1;Name=URF1;gbkey=Gene;gene=URF1;gene_biotype=protein_coding
MN544300.1 Genbank CDS 1544 1681 . + 0 ID=cds-QIA92680.1;Parent=gene-URF1;Dbxref=NCBI_GP:QIA92680.1;Name=QIA92680.1;Note=URF1;gbkey=CDS;gene=URF1;product=hypothetical protein;protein_id=QIA92680.1;transl_table=4
MN544300.1 Genbank gene 1684 2241 . + . ID=gene-COX2;Name=COX2;gbkey=Gene;gene=COX2;gene_biotype=protein_coding
MN544300.1 Genbank CDS 1684 2241 . + 0 ID=cds-QIA92681.1;Parent=gene-COX2;Dbxref=NCBI_GP:QIA92681.1;Name=QIA92681.1;Note=COX2;gbkey=CDS;gene=COX2;product=cytochrome c oxidase subunit II;protein_id=QIA92681.1;transl_table=4
MN544300.1 Genbank gene 2300 3637 . + . ID=gene-URF2;Name=URF2;gbkey=Gene;gene=URF2;gene_biotype=protein_coding
MN544300.1 Genbank CDS 2300 3637 . + 0 ID=cds-QIA92682.1;Parent=gene-URF2;Dbxref=NCBI_GP:QIA92682.1;Name=QIA92682.1;Note=URF2;gbkey=CDS;gene=URF2;product=hypothetical protein;protein_id=QIA92682.1;transl_table=4
MN544300.1 Genbank gene 3685 3828 . + . ID=gene-URF3;Name=URF3;gbkey=Gene;gene=URF3;gene_biotype=protein_coding
MN544300.1 Genbank CDS 3685 3828 . + 0 ID=cds-QIA92683.1;Parent=gene-URF3;Dbxref=NCBI_GP:QIA92683.1;Name=QIA92683.1;Note=URF3;gbkey=CDS;gene=URF3;product=hypothetical protein;protein_id=QIA92683.1;transl_table=4
MN544300.1 Genbank gene 4067 4999 . + . ID=gene-rnl;Name=rnl;gbkey=Gene;gene=rnl;gene_biotype=rRNA
MN544300.1 Genbank rRNA 4067 4999 . + . ID=rna-rnl;Parent=gene-rnl;Note=16S;gbkey=rRNA;gene=rnl;product=large subunit ribosomal RNA
MN544300.1 Genbank exon 4067 4999 . + . ID=exon-rnl-1;Parent=rna-rnl;Note=16S;gbkey=rRNA;gene=rnl;product=large subunit ribosomal RNA
MN544300.1 Genbank gene 5060 5646 . + . ID=gene-rns;Name=rns;gbkey=Gene;gene=rns;gene_biotype=rRNA
MN544300.1 Genbank rRNA 5060 5646 . + . ID=rna-rns;Parent=gene-rns;Note=12S;gbkey=rRNA;gene=rns;product=small subunit ribosomal RNA
MN544300.1 Genbank exon 5060 5646 . + . ID=exon-rns-1;Parent=rna-rns;Note=12S;gbkey=rRNA;gene=rns;product=small subunit ribosomal RNA
MN544300.1 Genbank gene 5673 6413 . + . ID=gene-COX3;Name=COX3;gbkey=Gene;gene=COX3;gene_biotype=protein_coding
MN544300.1 Genbank CDS 5673 6413 . + 0 ID=cds-QIA92684.1;Parent=gene-COX3;Dbxref=NCBI_GP:QIA92684.1;Name=QIA92684.1;Note=COX3;gbkey=CDS;gene=COX3;product=cytochrome c oxidase subunit III;protein_id=QIA92684.1;transl_table=4
MN544300.1 Genbank gene 6425 7141 . + . ID=gene-ND2;Name=ND2;gbkey=Gene;gene=ND2;gene_biotype=protein_coding
MN544300.1 Genbank CDS 6425 7141 . + 0 ID=cds-QIA92685.1;Parent=gene-ND2;Dbxref=NCBI_GP:QIA92685.1;Name=QIA92685.1;Note=ND2;gbkey=CDS;gene=ND2;product=NADH dehydrogenase subunit 2;protein_id=QIA92685.1;transl_table=4
MN544300.1 Genbank gene 7142 7450 . + . ID=gene-ND3;Name=ND3;gbkey=Gene;gene=ND3;gene_biotype=protein_coding
MN544300.1 Genbank CDS 7142 7450 . + 0 ID=cds-QIA92686.1;Parent=gene-ND3;Dbxref=NCBI_GP:QIA92686.1;Name=QIA92686.1;Note=ND3;gbkey=CDS;gene=ND3;product=NADH dehydrogenase subunit 3;protein_id=QIA92686.1;transl_table=4
MN544300.1 Genbank gene 7452 8534 . + . ID=gene-ND4;Name=ND4;gbkey=Gene;gene=ND4;gene_biotype=protein_coding
MN544300.1 Genbank CDS 7452 8534 . + 0 ID=cds-QIA92687.1;Parent=gene-ND4;Dbxref=NCBI_GP:QIA92687.1;Name=QIA92687.1;Note=ND4;gbkey=CDS;gene=ND4;product=NADH dehydrogenase subunit 4;protein_id=QIA92687.1;transl_table=4
MN544300.1 Genbank gene 8541 9644 . + . ID=gene-CYTB;Name=CYTB;gbkey=Gene;gene=CYTB;gene_biotype=protein_coding
MN544300.1 Genbank CDS 8541 9644 . + 0 ID=cds-QIA92688.1;Parent=gene-CYTB;Dbxref=NCBI_GP:QIA92688.1;Name=QIA92688.1;Note=CYTB;gbkey=CDS;gene=CYTB;product=cytochrome b;protein_id=QIA92688.1;transl_table=4
MN544300.1 Genbank gene 9651 11159 . + . ID=gene-ND5;Name=ND5;gbkey=Gene;gene=ND5;gene_biotype=protein_coding
MN544300.1 Genbank CDS 9651 11159 . + 0 ID=cds-QIA92689.1;Parent=gene-ND5;Dbxref=NCBI_GP:QIA92689.1;Name=QIA92689.1;Note=ND5;gbkey=CDS;gene=ND5;product=NADH dehydrogenase subunit 5;protein_id=QIA92689.1;transl_table=4
MN544300.1 Genbank gene 11162 11998 . + . ID=gene-ND1;Name=ND1;gbkey=Gene;gene=ND1;gene_biotype=protein_coding
MN544300.1 Genbank CDS 11162 11998 . + 0 ID=cds-QIA92690.1;Parent=gene-ND1;Dbxref=NCBI_GP:QIA92690.1;Name=QIA92690.1;Note=ND1;gbkey=CDS;gene=ND1;product=NADH dehydrogenase subunit 1;protein_id=QIA92690.1;transl_table=4
MN544300.1 Genbank gene 11998 12195 . + . ID=gene-ND6;Name=ND6;gbkey=Gene;gene=ND6;gene_biotype=protein_coding
MN544300.1 Genbank CDS 11998 12195 . + 0 ID=cds-QIA92691.1;Parent=gene-ND6;Dbxref=NCBI_GP:QIA92691.1;Name=QIA92691.1;Note=ND6;gbkey=CDS;gene=ND6;product=NADH dehydrogenase subunit 6;protein_id=QIA92691.1;transl_table=4
MN544300.1 Genbank gene 12197 12529 . + . ID=gene-ND4L;Name=ND4L;gbkey=Gene;gene=ND4L;gene_biotype=protein_coding
MN544300.1 Genbank CDS 12197 12529 . + 0 ID=cds-QIA92692.1;Parent=gene-ND4L;Dbxref=NCBI_GP:QIA92692.1;Name=QIA92692.1;Note=ND4L;gbkey=CDS;gene=ND4L;product=NADH dehydrogenase subunit 4L;protein_id=QIA92692.1;transl_table=4

38 changes: 38 additions & 0 deletions annotation/raw_files/Hc1_mito_Mrename.gff3
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##sequence-region M 1 12564
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1403702
M Genbank region 1 12564 . + . ID=M:1..12564;Dbxref=taxon:1403702;Is_circular=true;Name=MT;gbkey=Src;genome=mitochondrion;isolate=Hc1;mol_type=genomic DNA;note=BioSample: SAMN12924379
M Genbank gene 1 1539 . + . ID=gene-COX1;Name=COX1;gbkey=Gene;gene=COX1;gene_biotype=protein_coding
M Genbank CDS 1 1539 . + 0 ID=cds-QIA92679.1;Parent=gene-COX1;Dbxref=NCBI_GP:QIA92679.1;Name=QIA92679.1;Note=COX1;gbkey=CDS;gene=COX1;product=cytochrome c oxidase subunit I;protein_id=QIA92679.1;transl_table=4
M Genbank gene 1544 1681 . + . ID=gene-URF1;Name=URF1;gbkey=Gene;gene=URF1;gene_biotype=protein_coding
M Genbank CDS 1544 1681 . + 0 ID=cds-QIA92680.1;Parent=gene-URF1;Dbxref=NCBI_GP:QIA92680.1;Name=QIA92680.1;Note=URF1;gbkey=CDS;gene=URF1;product=hypothetical protein;protein_id=QIA92680.1;transl_table=4
M Genbank gene 1684 2241 . + . ID=gene-COX2;Name=COX2;gbkey=Gene;gene=COX2;gene_biotype=protein_coding
M Genbank CDS 1684 2241 . + 0 ID=cds-QIA92681.1;Parent=gene-COX2;Dbxref=NCBI_GP:QIA92681.1;Name=QIA92681.1;Note=COX2;gbkey=CDS;gene=COX2;product=cytochrome c oxidase subunit II;protein_id=QIA92681.1;transl_table=4
M Genbank gene 2300 3637 . + . ID=gene-URF2;Name=URF2;gbkey=Gene;gene=URF2;gene_biotype=protein_coding
M Genbank CDS 2300 3637 . + 0 ID=cds-QIA92682.1;Parent=gene-URF2;Dbxref=NCBI_GP:QIA92682.1;Name=QIA92682.1;Note=URF2;gbkey=CDS;gene=URF2;product=hypothetical protein;protein_id=QIA92682.1;transl_table=4
M Genbank gene 3685 3828 . + . ID=gene-URF3;Name=URF3;gbkey=Gene;gene=URF3;gene_biotype=protein_coding
M Genbank CDS 3685 3828 . + 0 ID=cds-QIA92683.1;Parent=gene-URF3;Dbxref=NCBI_GP:QIA92683.1;Name=QIA92683.1;Note=URF3;gbkey=CDS;gene=URF3;product=hypothetical protein;protein_id=QIA92683.1;transl_table=4
M Genbank gene 4067 4999 . + . ID=gene-rnl;Name=rnl;gbkey=Gene;gene=rnl;gene_biotype=rRNA
M Genbank rRNA 4067 4999 . + . ID=rna-rnl;Parent=gene-rnl;Note=16S;gbkey=rRNA;gene=rnl;product=large subunit ribosomal RNA
M Genbank exon 4067 4999 . + . ID=exon-rnl-1;Parent=rna-rnl;Note=16S;gbkey=rRNA;gene=rnl;product=large subunit ribosomal RNA
M Genbank gene 5060 5646 . + . ID=gene-rns;Name=rns;gbkey=Gene;gene=rns;gene_biotype=rRNA
M Genbank rRNA 5060 5646 . + . ID=rna-rns;Parent=gene-rns;Note=12S;gbkey=rRNA;gene=rns;product=small subunit ribosomal RNA
M Genbank exon 5060 5646 . + . ID=exon-rns-1;Parent=rna-rns;Note=12S;gbkey=rRNA;gene=rns;product=small subunit ribosomal RNA
M Genbank gene 5673 6413 . + . ID=gene-COX3;Name=COX3;gbkey=Gene;gene=COX3;gene_biotype=protein_coding
M Genbank CDS 5673 6413 . + 0 ID=cds-QIA92684.1;Parent=gene-COX3;Dbxref=NCBI_GP:QIA92684.1;Name=QIA92684.1;Note=COX3;gbkey=CDS;gene=COX3;product=cytochrome c oxidase subunit III;protein_id=QIA92684.1;transl_table=4
M Genbank gene 6425 7141 . + . ID=gene-ND2;Name=ND2;gbkey=Gene;gene=ND2;gene_biotype=protein_coding
M Genbank CDS 6425 7141 . + 0 ID=cds-QIA92685.1;Parent=gene-ND2;Dbxref=NCBI_GP:QIA92685.1;Name=QIA92685.1;Note=ND2;gbkey=CDS;gene=ND2;product=NADH dehydrogenase subunit 2;protein_id=QIA92685.1;transl_table=4
M Genbank gene 7142 7450 . + . ID=gene-ND3;Name=ND3;gbkey=Gene;gene=ND3;gene_biotype=protein_coding
M Genbank CDS 7142 7450 . + 0 ID=cds-QIA92686.1;Parent=gene-ND3;Dbxref=NCBI_GP:QIA92686.1;Name=QIA92686.1;Note=ND3;gbkey=CDS;gene=ND3;product=NADH dehydrogenase subunit 3;protein_id=QIA92686.1;transl_table=4
M Genbank gene 7452 8534 . + . ID=gene-ND4;Name=ND4;gbkey=Gene;gene=ND4;gene_biotype=protein_coding
M Genbank CDS 7452 8534 . + 0 ID=cds-QIA92687.1;Parent=gene-ND4;Dbxref=NCBI_GP:QIA92687.1;Name=QIA92687.1;Note=ND4;gbkey=CDS;gene=ND4;product=NADH dehydrogenase subunit 4;protein_id=QIA92687.1;transl_table=4
M Genbank gene 8541 9644 . + . ID=gene-CYTB;Name=CYTB;gbkey=Gene;gene=CYTB;gene_biotype=protein_coding
M Genbank CDS 8541 9644 . + 0 ID=cds-QIA92688.1;Parent=gene-CYTB;Dbxref=NCBI_GP:QIA92688.1;Name=QIA92688.1;Note=CYTB;gbkey=CDS;gene=CYTB;product=cytochrome b;protein_id=QIA92688.1;transl_table=4
M Genbank gene 9651 11159 . + . ID=gene-ND5;Name=ND5;gbkey=Gene;gene=ND5;gene_biotype=protein_coding
M Genbank CDS 9651 11159 . + 0 ID=cds-QIA92689.1;Parent=gene-ND5;Dbxref=NCBI_GP:QIA92689.1;Name=QIA92689.1;Note=ND5;gbkey=CDS;gene=ND5;product=NADH dehydrogenase subunit 5;protein_id=QIA92689.1;transl_table=4
M Genbank gene 11162 11998 . + . ID=gene-ND1;Name=ND1;gbkey=Gene;gene=ND1;gene_biotype=protein_coding
M Genbank CDS 11162 11998 . + 0 ID=cds-QIA92690.1;Parent=gene-ND1;Dbxref=NCBI_GP:QIA92690.1;Name=QIA92690.1;Note=ND1;gbkey=CDS;gene=ND1;product=NADH dehydrogenase subunit 1;protein_id=QIA92690.1;transl_table=4
M Genbank gene 11998 12195 . + . ID=gene-ND6;Name=ND6;gbkey=Gene;gene=ND6;gene_biotype=protein_coding
M Genbank CDS 11998 12195 . + 0 ID=cds-QIA92691.1;Parent=gene-ND6;Dbxref=NCBI_GP:QIA92691.1;Name=QIA92691.1;Note=ND6;gbkey=CDS;gene=ND6;product=NADH dehydrogenase subunit 6;protein_id=QIA92691.1;transl_table=4
M Genbank gene 12197 12529 . + . ID=gene-ND4L;Name=ND4L;gbkey=Gene;gene=ND4L;gene_biotype=protein_coding
M Genbank CDS 12197 12529 . + 0 ID=cds-QIA92692.1;Parent=gene-ND4L;Dbxref=NCBI_GP:QIA92692.1;Name=QIA92692.1;Note=ND4L;gbkey=CDS;gene=ND4L;product=NADH dehydrogenase subunit 4L;protein_id=QIA92692.1;transl_table=4

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