type: position_score
table:
  filename: ENCFF546KKI.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_ENCSR335JVB
  column_index: 3
  type: float
  desc: 'ATAC-seq ENCSR335JVB [biosample_summary="Homo sapiens GM19372"]'
  histogram:
    type: number
    number_of_bins: 100
meta:
  summary: 'ATAC-seq ENCSR335JVB [biosample_summary="Homo sapiens GM19372"]'
  description: "**status**: released\n\n**biological\\_replicates**: Rep 1\n\n**summary**:\
    \ \n\n**output\\_type**: pseudoreplicated peaks\n\n**audit\\_internal\\_action**:\
    \ Released analysis {ENCAN538AQP|/analyses/ENCAN538AQP/} has in progress subobject\
    \ quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/}\n\n\
    **audit\\_warning**: Alignment file {ENCFF301DFZ|/files/ENCFF301DFZ/} processed\
    \ by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 24491676 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 {ENCFF301DFZ|/files/ENCFF301DFZ/}\
    \ processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library\
    \ with NRF value of 0.857335.\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 {ENCFF301DFZ|/files/ENCFF301DFZ/} processed\
    \ by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with\
    \ a PBC1 value of 0.88."
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38
    accession: ENCSR335JVB
    status: released
    assay_term_name: ATAC-seq
    simple_biosample_summary: ''
    biosample_summary: Homo sapiens GM19372
    replication_type: unreplicated
    biosample_ontology: /biosample-types/cell_line_CLO_0027429/
    perturbed: false
    doi: 10.17989/ENCSR335JVB
    date_created: '2020-11-24T22:02:38.104909+00:00'
    date_released: '2021-02-11'
    submitter_comment: ''