type: position_score
table:
  filename: ENCFF934JPB.tabix.bed.gz
  header_mode: none
  zero_based: true
  format: tabix
  chrom:
    column_index: 0
  pos_begin:
    column_index: 1
  pos_end:
    column_index: 2
scores:
- id: ATAC-seq_ENCSR955JSO
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR955JSO [TISSUE: Homo sapiens breast epithelium tissue male
    adult (54 years)]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: male adult (54 years)


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN362BBC|/analyses/ENCAN362BBC/}
    has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}


    **audit\_internal\_action**: Released analysis {ENCAN362BBC|/analyses/ENCAN362BBC/}
    has in progress subobject document {72e5ee36-e11a-475d-a13a-8bda096d5636|/documents/72e5ee36-e11a-475d-a13a-8bda096d5636/}


    **audit\_not\_compliant**: According to ENCODE4 standards, overlap peaks files
    in ATAC-seq assays processed by the uniform processing pipeline should have FRiP
    (fraction of reads in called peak regions) scores > 0.3. FRiP scores 0.2-0.3 are
    acceptable, and < 0.2 are not compliant. {ENCFF934JPB|/files/ENCFF934JPB/} processed
    by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline  has a FRiP score of 0.12.


    **audit\_warning**: NRF (Non Redundant Fraction) is equal to the result of the
    division of the number of reads after duplicates removal by the total number of
    reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate
    complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but >
    0.7 is acceptable. ENCODE processed file {ENCFF344HVC|/files/ENCFF344HVC/} processed
    by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF
    value of 0.865547.


    **audit\_warning**: PBC1 (PCR Bottlenecking Coefficient 1, M1/M\_distinct) is
    the ratio of the number of genomic locations where  exactly one read maps uniquely
    (M1) to the number of genomic locations where some reads map (M\_distinct). A
    PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate
    bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking.
    PBC1 value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file
    {ENCFF344HVC|/files/ENCFF344HVC/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38
    pipeline was generated from a library with a PBC1 value of 0.87.


    **audit\_warning**: According to ENCODE4 standards, ATAC-seq assays processed
    by the uniform processing pipeline should have either >150k reproducible peaks
    in an overlap peaks file, or >70k in an IDR thresholded peaks file. 100-150k or
    50-70k peaks respectively is acceptable, and <100k or <50k respectively is not
    compliant. File(s) {ENCFF934JPB|/files/ENCFF934JPB/} (overlap peaks) and {ENCFF738IZU|/files/ENCFF738IZU/}
    (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have
    121178 and 62135 peaks.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR955JSO
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: male adult (54 years)
    biosample_summary: Homo sapiens breast epithelium tissue male adult (54 years)
    replication_type: unreplicated
    biosample_ontology: /biosample-types/tissue_UBERON_0008367/
    perturbed: false
    doi: 10.17989/ENCSR955JSO
    date_created: '2016-04-26T19:32:05.449699+00:00'
    date_released: '2016-06-15'
    submitter_comment: ''