type: position_score
table:
  filename: ENCFF883YXV.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_ENCSR635AIF
  column_index: 3
  type: float
  desc: 'ATAC-seq ENCSR635AIF [biosample_summary="Homo sapiens GM19468"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR635AIF [biosample_summary="Homo sapiens GM19468"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1\n\n**summary**:\
    \ \n\n**output\\_type**: pseudoreplicated peaks\n\n**audit\\_error**: Alignment\
    \ file {ENCFF362ACE|/files/ENCFF362ACE/} processed by ATAC-seq ENCODE4 v1.9.1\
    \ GRCh38 pipeline has 6496961 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\\_internal\\_action**: Released analysis {ENCAN496PIY|/analyses/ENCAN496PIY/}\
    \ has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}\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 {ENCFF362ACE|/files/ENCFF362ACE/}\
    \ processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.834628.\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 {ENCFF362ACE|/files/ENCFF362ACE/} processed\
    \ by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with\
    \ a PBC1 value of 0.83.\n\n**audit\\_warning**: According to ENCODE4 standards,\
    \ ATAC-seq assays processed by the uniform processing pipeline should have either\
    \ >150k reproducible peaks in an overlap peaks file, or >70k in an IDR thresholded\
    \ peaks file. 100-150k or 50-70k peaks respectively is acceptable, and <100k or\
    \ <50k respectively is not compliant. File(s) {ENCFF883YXV|/files/ENCFF883YXV/}\
    \ (overlap peaks) and {ENCFF550WFX|/files/ENCFF550WFX/} (IDR thresholded peaks)\
    \ processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline have 88727 and 51568 peaks."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR635AIF
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens GM19468
    replication_type: unreplicated
    biosample_ontology: /biosample-types/cell_line_CLO_0026875/
    perturbed: false
    doi: 10.17989/ENCSR635AIF
    date_created: '2020-11-24T22:02:39.229541+00:00'
    date_released: '2021-02-11'
    submitter_comment: ''