type: position_score
table:
  filename: ENCFF194RXY.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_ENCSR245QTD
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR245QTD [biosample_summary="Homo sapiens stomach tissue male child (3 years)" and target="H3K4me1"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR245QTD [biosample_summary="Homo sapiens stomach tissue male child (3 years)" and target="H3K4me1"]'
  description: '**status**: released


    **biological\_replicates**: Rep 1


    **summary**: male child (3 years)


    **output\_type**: pseudoreplicated peaks


    **audit\_internal\_action**: Archived analysis {ENCAN760DTB|/analyses/ENCAN760DTB/}
    has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/}


    **audit\_not\_compliant**: Processed alignments file {ENCFF430ERF|/files/ENCFF430ERF/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10864515 usable fragments. The
    minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting
    H3K4me1-human and investigated as a broad histone mark is 20 million usable fragments.
    The recommended value is > 45 million, but > 35 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 {ENCFF430ERF|/files/ENCFF430ERF/}
    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 {ENCFF430ERF|/files/ENCFF430ERF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline
    was generated from a library with PBC1 value of 0.76.


    **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 {ENCFF430ERF|/files/ENCFF430ERF/}
    processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with
    PBC2 value of 4.50.'
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR245QTD
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: male child (3 years)
    biosample_summary: Homo sapiens stomach tissue male child (3 years)
    replication_type: unreplicated
    biosample_ontology: /biosample-types/tissue_UBERON_0000945/
    perturbed: false
    doi: 10.17989/ENCSR245QTD
    date_created: '2015-10-01T07:17:10.704293+00:00'
    date_released: '2013-07-31'
    submitter_comment: ''
    target: H3K4me1