type: position_score
table:
  filename: ENCFF039JXQ.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: TF_ChIP-seq_ENCSR919UCY
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR919UCY [TISSUE: Homo sapiens vagina tissue female adult
    (53 years), TARGET: POLR2AphosphoS5]'
  description: '**status**: archived


    **biological\_replicates**: Rep 1


    **summary**: female adult (53 years)


    **output\_type**: pseudoreplicated IDR thresholded peaks


    **audit\_internal\_action**: Archived analysis {ENCAN395ENN|/analyses/ENCAN395ENN/}
    has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}


    **audit\_warning**: Processed alignments file {ENCFF246PZZ|/files/ENCFF246PZZ/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10836558 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    POLR2AphosphoS5-human and investigated as a transcription factor is 10 million
    usable fragments. The recommended value is > 20 million, but > 10 million is acceptable.
    (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/} )


    **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 in the range 0 - 0.5 is poor complexity, 0.5 - 0.8 is moderate
    complexity, and > 0.8 high complexity. NRF value > 0.8 is recommended, but > 0.5
    is acceptable. ENCODE processed alignments file {ENCFF246PZZ|/files/ENCFF246PZZ/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    NRF value of 0.80.


    **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 > 0.8 is acceptable. ENCODE processed alignments
    file {ENCFF246PZZ|/files/ENCFF246PZZ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.82.


    **audit\_warning**: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio
    of the number of genomic locations where exactly one read maps uniquely (M1) to
    the number of genomic locations where two reads map uniquely (M2). A PBC2 value
    in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3
    - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended,
    but > 3 is acceptable. ENCODE processed alignments file {ENCFF246PZZ|/files/ENCFF246PZZ/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 6.00.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR919UCY
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: female adult (53 years)
    biosample_summary: Homo sapiens vagina tissue female adult (53 years)
    replication_type: unreplicated
    biosample_ontology: /biosample-types/tissue_UBERON_0000996/
    perturbed: false
    doi: 10.17989/ENCSR919UCY
    date_created: '2017-01-31T16:16:23.057885+00:00'
    date_released: '2017-10-31'
    submitter_comment: Duplication of reads found in older fastqs. Files and analyses
      that are processed with corrected fastqs were done in 2021.
    target: POLR2AphosphoS5