type: position_score
table:
  filename: ENCFF688UTO.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_ENCSR318GET
  column_index: 3
  type: float
  desc: 'TF_ChIP-seq ENCSR318GET [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens HOXA9" and target="HOXA9"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'TF_ChIP-seq ENCSR318GET [biosample_summary="Homo sapiens HepG2 genetically modified (insertion) using CRISPR targeting H. sapiens HOXA9" and target="HOXA9"]'
  description: '**status**: released


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


    **summary**: genetically modified (insertion) using CRISPR targeting H. sapiens
    HOXA9


    **output\_type**: IDR thresholded peaks


    **audit\_internal\_action**: Released analysis {ENCAN589FDZ|/analyses/ENCAN589FDZ/}
    has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-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 {ENCFF658PCB|/files/ENCFF658PCB/}
    processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline was generated from a library
    with NRF value of 0.78.


    **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 {ENCFF658PCB|/files/ENCFF658PCB/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.78.


    **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 {ENCFF658PCB|/files/ENCFF658PCB/}
    processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 4.63.


    **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 {ENCFF905STU|/files/ENCFF905STU/}
    processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline was generated from a library
    with NRF value of 0.77.


    **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 {ENCFF905STU|/files/ENCFF905STU/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38
    pipeline was generated from a library with PBC1 value of 0.77.


    **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 {ENCFF905STU|/files/ENCFF905STU/}
    processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline was generated from a library
    with PBC2 value of 4.32.


    **audit\_warning**: Replicate concordance in ChIP-seq experiments is measured
    by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR
    thresholded peaks files {ENCFF688UTO|/files/ENCFF688UTO/} processed by ChIP-seq
    ENCODE4 v1.8.1 GRCh38 pipeline have a rescue ratio of 1.18 and a self consistency
    ratio of 2.18. According to ENCODE standards, having both rescue ratio and self
    consistency ratio values < 2 is recommended, but having only one of the ratio
    values < 2 is acceptable.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR318GET
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: genetically modified (insertion) using CRISPR targeting
      H. sapiens HOXA9
    biosample_summary: Homo sapiens HepG2 genetically modified (insertion) using CRISPR
      targeting H. sapiens HOXA9
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001187/
    perturbed: false
    doi: 10.17989/ENCSR318GET
    date_created: '2022-08-10T14:54:52.914475+00:00'
    date_released: '2022-09-30'
    submitter_comment: ''
    target: HOXA9