type: position_score
table:
  filename: ENCFF421XIL.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_ENCSR603LVR
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR603LVR [TISSUE: Homo sapiens B cell male adult (22 years)]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: male adult (22 years)


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN851QNO|/analyses/ENCAN851QNO/}
    has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}


    **audit\_warning**: Alignment file {ENCFF060ZGV|/files/ENCFF060ZGV/} processed
    by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 21836765 usable fragments. According
    to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline
    should have > 25 million usable fragments. 20-25 million is acceptable and < 15
    million is not compliant.


    **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 {ENCFF060ZGV|/files/ENCFF060ZGV/} processed
    by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with
    NRF value of 0.730072.


    **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
    {ENCFF060ZGV|/files/ENCFF060ZGV/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38
    pipeline was generated from a library with a PBC1 value of 0.75.


    **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) {ENCFF421XIL|/files/ENCFF421XIL/} (overlap peaks) and {ENCFF390ASB|/files/ENCFF390ASB/}
    (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline
    have 100655 and 68214 peaks.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR603LVR
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: male adult (22 years)
    biosample_summary: Homo sapiens B cell male adult (22 years)
    replication_type: unreplicated
    biosample_ontology: /biosample-types/primary_cell_CL_0000236/
    perturbed: false
    doi: 10.17989/ENCSR603LVR
    date_created: '2020-10-30T22:44:56.565396+00:00'
    date_released: '2021-06-24'
    submitter_comment: ''
