type: position_score
table:
  filename: ENCFF348XSG.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_ENCSR242QRV
  column_index: 3
  type: float
  desc: 'ATAC-seq ENCSR242QRV [biosample_summary="Homo sapiens upper lobe of left lung tissue female adult (61 years)"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR242QRV [biosample_summary="Homo sapiens upper lobe of left lung tissue female adult (61 years)"]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: female adult (61 years)


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN747ETK|/analyses/ENCAN747ETK/}
    has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}


    **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. {ENCFF348XSG|/files/ENCFF348XSG/} processed
    by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline  has a FRiP score of 0.09.


    **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 {ENCFF225GIF|/files/ENCFF225GIF/} processed
    by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF
    value of 0.892108.


    **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
    {ENCFF225GIF|/files/ENCFF225GIF/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38
    pipeline was generated from a library with a PBC1 value of 0.90.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR242QRV
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: female adult (61 years)
    biosample_summary: Homo sapiens upper lobe of left lung tissue female adult (61
      years)
    replication_type: unreplicated
    biosample_ontology: /biosample-types/tissue_UBERON_0008952/
    perturbed: false
    doi: 10.17989/ENCSR242QRV
    date_created: '2019-07-30T07:42:46.910612+00:00'
    date_released: '2022-06-16'
    submitter_comment: Despite lower enrichment scores and peaks, sequence-based predictive
      models (neural networks) fit to these data reveal useful motifs and motif annotations.
      Given the value of these rare samples, we release them with an enrichment QC
      warning indicating that these data likely have lower sensitivity for detecting
      accessible regulatory elements.