type: position_score
table:
  filename: ENCFF272UZC.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_ENCSR866KFY
  column_index: 3
  type: float
  desc: 'Histone_ChIP-seq ENCSR866KFY [biosample_summary="Homo sapiens GM23248" and target="H3K27me3"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'Histone_ChIP-seq ENCSR866KFY [biosample_summary="Homo sapiens GM23248" and target="H3K27me3"]'
  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 {ENCAN646SHM|/analyses/ENCAN646SHM/} has in progress\
    \ subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/}\n\
    \n**audit\\_not\\_compliant**: Processed alignments file {ENCFF122SGX|/files/ENCFF122SGX/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 32287940 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K27me3-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/})\n\n**audit\\\
    _not\\_compliant**: Processed alignments file {ENCFF943RTB|/files/ENCFF943RTB/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline has 33129669 usable fragments.\
    \ The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting\
    \ H3K27me3-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/})\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 alignments file\
    \ {ENCFF122SGX|/files/ENCFF122SGX/} processed by ChIP-seq ENCODE3 GRCh38 pipeline\
    \ was generated from a library with PBC1 value of 0.83.\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 alignments file {ENCFF122SGX|/files/ENCFF122SGX/}\
    \ processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with\
    \ PBC2 value of 5.66.\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 alignments file {ENCFF943RTB|/files/ENCFF943RTB/} processed\
    \ by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value\
    \ of 0.88.\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 alignments\
    \ file {ENCFF943RTB|/files/ENCFF943RTB/} processed by ChIP-seq ENCODE3 GRCh38\
    \ pipeline was generated from a library with PBC2 value of 8.02."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR866KFY
    status: released
    assay_term_name: ChIP-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens GM23248
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0005723/
    perturbed: false
    doi: 10.17989/ENCSR866KFY
    date_created: '2014-10-24T16:26:17.120822+00:00'
    date_released: '2016-05-03'
    submitter_comment: 'Fastq file ENCFF514XBK contains conflicting read lengths between
      data and metadata; read lengths followed by respective number of reads: (25,
      64207064). Fastq file ENCFF143XTU contains conflicting read lengths between
      data and metadata; read lengths followed by respective number of reads: (36,
      25355178). Fastq file ENCFF282HVQ contains conflicting read lengths between
      data and metadata; read lengths followed by respective number of reads: (25,
      25355178). Fastq file ENCFF206FVJ specified read length was 25, but the file
      contains read length(s) (25, 44859225), (36, 25355178).  As of January 9th,
      2018, metadata has been changed to reflect the data.'
    target: H3K27me3