type: position_score
table:
  filename: ENCFF725WVP.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_ENCSR224NFP
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR224NFP [biosample_summary="Homo sapiens HEK293 genetically modified (insertion) using site-specific recombination targeting H. sapiens ZNF426" and target="ZNF426"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR224NFP [biosample_summary="Homo sapiens HEK293 genetically modified (insertion) using site-specific recombination targeting H. sapiens ZNF426" and target="ZNF426"]'
  description: '**status**: released


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


    **summary**: genetically modified (insertion) using site-specific recombination
    targeting H. sapiens ZNF426


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


    **audit\_internal\_action**: File {ENCFF725WVP|/files/ENCFF725WVP/} with status
    ''released'' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status
    ''archived''.


    **audit\_internal\_action**: Archived analysis {ENCAN615LJI|/analyses/ENCAN615LJI/}
    has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/}


    **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 {ENCFF846ILV|/files/ENCFF846ILV/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    NRF value of 0.75.


    **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 {ENCFF846ILV|/files/ENCFF846ILV/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.75.


    **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 {ENCFF846ILV|/files/ENCFF846ILV/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 4.00.


    **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 {ENCFF021UNS|/files/ENCFF021UNS/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    NRF value of 0.72.


    **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 {ENCFF021UNS|/files/ENCFF021UNS/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.72.


    **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 {ENCFF021UNS|/files/ENCFF021UNS/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 3.57.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR224NFP
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: genetically modified (insertion) using site-specific
      recombination targeting H. sapiens ZNF426
    biosample_summary: Homo sapiens HEK293 genetically modified (insertion) using
      site-specific recombination targeting H. sapiens ZNF426
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001182/
    perturbed: false
    doi: 10.17989/ENCSR224NFP
    date_created: '2016-03-29T17:49:52.630187+00:00'
    date_released: '2017-03-16'
    submitter_comment: The archived libraries sequenced on HiSeq 2000 did not meet
      ENCODE read depth requirements. We have therefore provided more deeply sequenced
      data on HiSeq 4000.
    target: ZNF426