Resource
| Id | TF_ChIP-seq/ENCSR000AQK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000AQK [biosample_summary="Homo sapiens H1" and target="CHD1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN020HYO|/analyses/ENCAN020HYO/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF617RGJ|/files/ENCFF617RGJ/}, {ENCFF693GHB|/files/ENCFF693GHB/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 2.47 and a self consistency ratio of 6.00. According to ENCODE standards, having both rescue ratio and self consistency ratio values < 2 is recommended, but having only one of the ratio values < 2 is acceptable. audit_not_compliant: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF741MOG|/files/ENCFF741MOG/}, {ENCFF735ZAF|/files/ENCFF735ZAF/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 2.47 and a self consistency ratio of 6.00. According to ENCODE standards, having both rescue ratio and self consistency ratio values < 2 is recommended, but having only one of the ratio values < 2 is acceptable. 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 {ENCFF847WER|/files/ENCFF847WER/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF847WER|/files/ENCFF847WER/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 5.81. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000AQK | float |
TF_ChIP-seq_ENCSR000AQK |
TF_ChIP-seq ENCSR000AQK [biosample_summary="Homo sapiens H1" and target="CHD1"]
|
 |
[10.9, 327] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4510312 | 0.14% | 10918 |
| chr1 | 461797 | 0.19% | 1143 |
| chr2 | 322203 | 0.13% | 793 |
| chr3 | 262740 | 0.13% | 607 |
| chr4 | 213877 | 0.11% | 538 |
| chr5 | 257984 | 0.14% | 640 |
| chr6 | 386614 | 0.23% | 808 |
| chr7 | 221281 | 0.14% | 544 |
| chr8 | 195602 | 0.13% | 504 |
| chr9 | 161416 | 0.12% | 435 |
| chr10 | 189364 | 0.14% | 460 |
| chr11 | 247816 | 0.18% | 590 |
| chr12 | 267468 | 0.20% | 663 |
| chr13 | 103752 | 0.09% | 267 |
| chr14 | 166487 | 0.16% | 417 |
| chr15 | 140543 | 0.14% | 333 |
| chr16 | 141822 | 0.16% | 331 |
| chr17 | 231383 | 0.28% | 559 |
| chr18 | 73868 | 0.09% | 181 |
| chr19 | 195239 | 0.33% | 479 |
| chr20 | 109103 | 0.17% | 252 |
| chr21 | 29931 | 0.06% | 74 |
| chr22 | 71222 | 0.14% | 164 |
| chrX | 58800 | 0.04% | 136 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 10918 | 1 | 7626 | 413.11 | 378 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF617RGJ.bed.gz | 164.39 KB | 26d5177bf6655b63dcbaf3942dbc9702 |
| ENCFF617RGJ.tabix.bed.gz | 125.96 KB | 4c8ee23d9235c7318a6f8d384842a792 |
| ENCFF617RGJ.tabix.bed.gz.tbi | 56.22 KB | 7296a381fafe727f9a550d01888371eb |
| genomic_resource.yaml | 3.87 KB | 8efccfb31374f87cbe220e2f35dc34d2 |
| statistics/ |