type: position_score
table:
  filename: ENCFF296LMD.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_ENCSR414DVK
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR414DVK [TISSUE: Homo sapiens adrenal gland tissue female
    adult (51 years)]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: female adult (51 years)


    **output\_type**: pseudoreplicated peaks


    **audit\_error**: Alignment file {ENCFF946URK|/files/ENCFF946URK/} processed by
    ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 12122240 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\_internal\_action**: Released analysis {ENCAN481VYZ|/analyses/ENCAN481VYZ/}
    has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}


    **audit\_internal\_action**: Released analysis {ENCAN481VYZ|/analyses/ENCAN481VYZ/}
    has in progress subobject document {49215c69-33db-4187-b5f6-c9c77a2cafb7|/documents/49215c69-33db-4187-b5f6-c9c77a2cafb7/}


    **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. {ENCFF296LMD|/files/ENCFF296LMD/} processed
    by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline  has a FRiP score of 0.12.


    **audit\_not\_compliant**: 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) {ENCFF296LMD|/files/ENCFF296LMD/} (overlap peaks) and {ENCFF663KQH|/files/ENCFF663KQH/}
    (IDR thresholded peaks) processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have
    81117 and 32318 peaks.


    **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 {ENCFF946URK|/files/ENCFF946URK/} processed
    by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF
    value of 0.896244.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR414DVK
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: female adult (51 years)
    biosample_summary: Homo sapiens adrenal gland tissue female adult (51 years)
    replication_type: unreplicated
    biosample_ontology: /biosample-types/tissue_UBERON_0002369/
    perturbed: false
    doi: 10.17989/ENCSR414DVK
    date_created: '2017-02-07T01:37:27.378145+00:00'
    date_released: '2017-03-09'
    submitter_comment: ''