type: position_score
table:
  filename: ENCFF296VDQ.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_ENCSR000DUQ
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR000DUQ [biosample_summary="Homo sapiens mammary epithelial cell female" and target="H3K4me3"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR000DUQ [biosample_summary="Homo sapiens mammary epithelial cell female" and target="H3K4me3"]'
  description: '**status**: released


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


    **summary**: female


    **output\_type**: replicated peaks


    **audit\_internal\_action**: Archived analysis {ENCAN687DIN|/analyses/ENCAN687DIN/}
    has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/}


    **audit\_warning**: Processed alignments file {ENCFF029KZM|/files/ENCFF029KZM/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13184720 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H3K4me3-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 {ENCFF995CUR|/files/ENCFF995CUR/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17156259 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H3K4me3-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 {ENCFF029KZM|/files/ENCFF029KZM/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.85.


    **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 {ENCFF029KZM|/files/ENCFF029KZM/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 7.29.


    **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 {ENCFF995CUR|/files/ENCFF995CUR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.83.


    **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 {ENCFF995CUR|/files/ENCFF995CUR/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 6.40.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR000DUQ
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: female
    biosample_summary: Homo sapiens mammary epithelial cell female
    replication_type: isogenic
    biosample_ontology: /biosample-types/primary_cell_CL_0002327/
    perturbed: false
    doi: 10.17989/ENCSR000DUQ
    date_created: '2014-02-12T23:14:08.242627+00:00'
    date_released: '2011-02-11'
    submitter_comment: Replicate 1,1 of this experiment was previously attributed
      to biosample ENCBS090ENC but it has since been corrected to the current biosample.
      Please note that the biosample term has remain unchanged.
    target: H3K4me3