type: position_score
table:
  filename: ENCFF424JEX.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_ENCSR685OFR
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR685OFR [TISSUE: Homo sapiens naive B cell female adult (39
    years)]'
  description: '**status**: released


    **biological\_replicates**: Rep 1, Rep 2


    **summary**: female adult (39 years)


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Released analysis {ENCAN160XVS|/analyses/ENCAN160XVS/}
    has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}


    **audit\_warning**: Alignment file {ENCFF402TQJ|/files/ENCFF402TQJ/} processed
    by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 22532527 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**: Alignment file {ENCFF271LEW|/files/ENCFF271LEW/} processed
    by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline has 21039551 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 {ENCFF402TQJ|/files/ENCFF402TQJ/} processed
    by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with
    NRF value of 0.847443.


    **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
    {ENCFF402TQJ|/files/ENCFF402TQJ/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38
    pipeline was generated from a library with a PBC1 value of 0.87.


    **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 {ENCFF271LEW|/files/ENCFF271LEW/} processed
    by ATAC-seq ENCODE4 v1.10.0 GRCh38 pipeline was generated from a library with
    NRF value of 0.848575.


    **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
    {ENCFF271LEW|/files/ENCFF271LEW/} processed by ATAC-seq ENCODE4 v1.10.0 GRCh38
    pipeline was generated from a library with a PBC1 value of 0.88.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR685OFR
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: female adult (39 years)
    biosample_summary: Homo sapiens naive B cell female adult (39 years)
    replication_type: isogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0000788/
    perturbed: false
    doi: 10.17989/ENCSR685OFR
    date_created: '2021-08-25T22:17:08.713303+00:00'
    date_released: '2021-09-09'
    submitter_comment: ''
