type: position_score
table:
  filename: ENCFF913MQB.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: ATAC-seq_ENCSR042AWH
  column_index: 3
  type: float
  desc: 'ATAC-seq ENCSR042AWH [biosample_summary="Homo sapiens HepG2"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR042AWH [biosample_summary="Homo sapiens HepG2"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1, Rep 2\n\
    \n**summary**: \n\n**output\\_type**: pseudoreplicated peaks\n\n**audit\\_internal\\\
    _action**: Released analysis {ENCAN074ZCE|/analyses/ENCAN074ZCE/} has in progress\
    \ subobject document {23706428-f8ac-4cfe-a00a-75c4fc032407|/documents/23706428-f8ac-4cfe-a00a-75c4fc032407/}\n\
    \n**audit\\_internal\\_action**: Released analysis {ENCAN074ZCE|/analyses/ENCAN074ZCE/}\
    \ has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}\n\
    \n**audit\\_warning**: Alignment file {ENCFF239RGZ|/files/ENCFF239RGZ/} processed\
    \ by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 23501715 usable fragments. According\
    \ to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline\
    \ should have > 25 million usable fragments. 20-25 million is acceptable and <\
    \ 15 million is not compliant.\n\n**audit\\_warning**: Alignment file {ENCFF394BBD|/files/ENCFF394BBD/}\
    \ processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 23241010 usable fragments.\
    \ According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing\
    \ pipeline should have > 25 million usable fragments. 20-25 million is acceptable\
    \ and < 15 million is not compliant.\n\n**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 < 0.7 is poor\
    \ complexity, between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity.\
    \ NRF value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file\
    \ {ENCFF239RGZ|/files/ENCFF239RGZ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38\
    \ pipeline was generated from a library with NRF value of 0.80483.\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 > 0.7 is acceptable. ENCODE processed file {ENCFF239RGZ|/files/ENCFF239RGZ/}\
    \ processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library\
    \ with a PBC1 value of 0.82.\n\n**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 < 0.7 is poor complexity,\
    \ between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF\
    \ value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF394BBD|/files/ENCFF394BBD/}\
    \ processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.809794.\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 > 0.7 is\
    \ acceptable. ENCODE processed file {ENCFF394BBD|/files/ENCFF394BBD/} processed\
    \ by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with\
    \ a PBC1 value of 0.82."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR042AWH
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens HepG2
    replication_type: isogenic
    biosample_ontology: /biosample-types/cell_line_EFO_0001187/
    perturbed: false
    doi: 10.17989/ENCSR042AWH
    date_created: '2020-05-18T11:20:05.770586+00:00'
    date_released: '2020-08-05'
    submitter_comment: ''