type: position_score
table:
  filename: ENCFF556TDW.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_ENCSR550GSE
  column_index: 3
  type: float
  desc: signal
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ChIP-seq ENCSR550GSE [TISSUE: Homo sapiens UCSF-4, TARGET: H3K9me3]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: replicated peaks\n\n**audit\\_internal\\\
    _action**: Archived analysis {ENCAN129XCY|/analyses/ENCAN129XCY/} has in progress\
    \ subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed redacted unfiltered alignments file {ENCFF860CKW|/files/ENCFF860CKW/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 31777781 mapped reads. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K9me3-human and investigated as a broad histone mark is 35 million mapped\
    \ reads. The recommended value is > 45 million, but > 35 million is acceptable.\
    \ (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/})\n\n**audit\\\
    _not\\_compliant**: Processed redacted unfiltered alignments file {ENCFF138RRZ|/files/ENCFF138RRZ/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18784821 mapped reads. The\
    \ minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K9me3-human and investigated as a broad histone mark is 35 million mapped\
    \ reads. The recommended value is > 45 million, but > 35 million is acceptable.\
    \ (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/})\n\n**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 redacted alignments\
    \ file {ENCFF044UQK|/files/ENCFF044UQK/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC1 value of 0.89.\n\n**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 redacted alignments file {ENCFF044UQK|/files/ENCFF044UQK/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 9.55."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR550GSE
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens UCSF-4
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0007116/
    perturbed: false
    doi: 10.17989/ENCSR550GSE
    date_created: '2015-09-15T20:27:09.885190+00:00'
    date_released: '2013-07-31'
    submitter_comment: ''
    target: H3K9me3