type: position_score
table:
  filename: ENCFF005LQD.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: Histone_ChIP-seq_ENCSR000ATG
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR000ATG [biosample_summary="Homo sapiens fibroblast of dermis NONE and female adult" and target="H2AFZ"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR000ATG [biosample_summary="Homo sapiens fibroblast of dermis NONE and female adult" and target="H2AFZ"]'
  description: '**status**: released


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


    **summary**:  female adult


    **output\_type**: replicated peaks


    **audit\_internal\_action**: Archived analysis {ENCAN745IVJ|/analyses/ENCAN745IVJ/}
    has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/}


    **audit\_warning**: Processed alignments file {ENCFF515NLW|/files/ENCFF515NLW/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 16857187 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H2AFZ-human and investigated as a narrow histone mark 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**: Processed alignments file {ENCFF065NBX|/files/ENCFF065NBX/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18063926 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H2AFZ-human and investigated as a narrow histone mark 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**: 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 {ENCFF515NLW|/files/ENCFF515NLW/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.88.


    **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 {ENCFF515NLW|/files/ENCFF515NLW/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 8.36.


    **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 {ENCFF065NBX|/files/ENCFF065NBX/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    NRF value of 0.62.


    **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 {ENCFF065NBX|/files/ENCFF065NBX/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.60.


    **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 {ENCFF065NBX|/files/ENCFF065NBX/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 2.35.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000ATG
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ' female adult'
    biosample_summary: Homo sapiens fibroblast of dermis NONE and female adult
    replication_type: anisogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0002551/
    perturbed: false
    doi: 10.17989/ENCSR000ATG
    date_created: '2013-11-07T22:15:54.603920+00:00'
    date_released: '2012-08-06'
    submitter_comment: This experiment requires new peak calling due to new data from
      its control, ENCSR000APT.
    target: H2AFZ