DOI: 10.6084/m9.figshare.22100825
title: Chromatin accessibility associated with aquaculture relevant traits in Nile tilapia - Data applicable to the study

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<strong>## We provide data relevant to the publication, summarised as:</strong>
# 1. BED file of O. niloticus CNE annotations
# 2. Annotated gill peaks
# 3. Overlap of annotated gill peaks with SNPs
# 4. Gene promoter TFBS footprints with gill SNP-peaks
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<strong>### 1. </strong><em><strong>O. niloticus </strong></em><strong>(Nile tilapia) annotated CNEs</strong>
## File: Oreochromis_niloticus.UMD_NMBU.CNE.annot.bed
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## Columns are:
# 1. CNE chromosome/scaffold
# 2. CNE start
# 3. CNE end
# 4. CNE type: Average_Conservation Score &gt;=0.9 = hCNE; aCNE = Average_Conservation Score &lt;0.9, deviating from the neutral model, and so have a negative CONACC score, lnl ratio &lt;0.05, and significant divergence (altsubscale &gt;1)
# 5. CNE score (all = .)
# 6. CNE strand
# 7. closest Ensembl Gene ID
# 8. Ensembl Transcript ID (all = .)
# 9. CNE details - Total conservation score (PhastCons); length of CNE; Average_Conservation Score (PhastCons); Gene distance from CNE
# 10. closest gene symbol
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<strong>### 2. Collated replicate gill open chromatin peaks intersected with annotation features - all IDR true and false peaks provided</strong>
## File: On_G_ATAC_peaks.collated.narrowPeak.features.gff
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## Columns are:
# 1: peak chromosome/scaffold
# 2: peak ID
# 3: peak feature
# 4: peak start
# 5: peak end
# 6: peak score
# 7: peak strand
# 8. feature frame
# 9: peak calling details from MACS2 (; separated)
  # a. signal value - measurement of overall enrichment for the region
  # b. p-val - stat significance (-log10)
  # c. q-val - stat significance using FDR (-log10)
  # d. peak - point-source called for this peak; 0-based offset from chromStart (like the peak summit)
  # e. IDR - true or false for reproducibility between replicates
  # f. ensemblID for gene promoter
  # g. gene symbol
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<strong>### 3. Collated replicate gill open chromatin peaks annotated by feature and intersected with tilapia SNPs</strong>
## File: On_G_ATAC_peaks.collated.narrowPeak.features.intersectSNPs.bed
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## Columns are:
# 1: SNP chromosome/scaffold
# 2: SNP start
# 3: SNP end
# 4: SNP ID
# 5: SNP score
# 6: SNP strand
# 7: SNP feature (all '5kb_gene_promoter')
# 8: SNP gene annotation (from GTF)
# 9: peak chr
# 10: peak start
# 11: peak end
# 12: peak ID
# 13: peak score
# 14: peak strand
# 15: peak feature
# 16: peak calling details from MACS2 (; separated)
  # a. signal value - measurement of overall enrichment for the region
  # b. p-val - stat significance (-log10)
  # c. q-val - stat significance using FDR (-log10)
  # d. peak - point-source called for this peak; 0-based offset from chromStart (like the peak summit)
  # e. IDR - true or false for reproducibility between replicates
  # f. ensemblID for gene promoter
  # g. gene symbol
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<strong>### 4. Gene promoter TFBS footprints with gill SNP-peaks (from collated replicate peaks - all IDR true and false peaks provided)</strong>
## File: On_G_ATAC_mpbs_GenePromfpSNPATAC.txt
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## Columns are:
# 1: SNP chromosome/scaffold
# 2: SNP start
# 3: SNP end
# 4: SNP ID
# 5: SNP score
# 6: SNP strand
# 7: SNP feature (all '5kb_gene_promoter')
# 8: SNP gene annotation (from GTF?)
# 9: peak chromosome/scaffold
# 10: peak start
# 11: peak end
# 12: peak ID
# 13: peak score
# 14: peak strand
# 15: peak feature (all '5kb_gene_promoter')
# 16: peak calling details from MACS2 (; separated)
  # a. signal value - measurement of overall enrichment for the region
  # b. p-val - stat significance (-log10)
  # c. q-val - stat significance using FDR (-log10)
  # d. peak - point-source called for this peak; 0-based offset from chromStart (like the peak summit)
  # e. IDR - true or false
  # f. ensemblID for gene promoter
  # g. gene symbol
# 17: presence/absence - all present
# 18: TFBS chromosome/scaffold
# 19: TFBS start
# 20: TFBS end
# 21: TFBS ID
# 22: bit-score of motif match
# 23: TFBS strand
# 24: footprint chr
# 25: footprint start
# 26: footprint end
# 27: footprint ID
# 28: footprint tag count (TC)
# 29: footprint strand - all are .
# 30: TFBS and footprint overlap