Resource
| Id | TF_ChIP-seq/ENCSR000BHN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BHN [biosample_summary="Homo sapiens H1" and target="POLR2A"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN723OCC|/analyses/ENCAN723OCC/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF526YGE|/files/ENCFF526YGE/} processed by ChIP-seq ENCODE3 hg19 pipeline has 19855551 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting POLR2A-human and investigated as a transcription factor is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/} ) 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 {ENCFF526YGE|/files/ENCFF526YGE/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF526YGE|/files/ENCFF526YGE/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.82. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BHN | float |
TF_ChIP-seq_ENCSR000BHN |
TF_ChIP-seq ENCSR000BHN [biosample_summary="Homo sapiens H1" and target="POLR2A"]
|
 |
[9.16, 639] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 17449814 | 0.54% | 41877 |
| chr1 | 1800121 | 0.72% | 4316 |
| chr2 | 1107553 | 0.46% | 2618 |
| chr3 | 1002512 | 0.51% | 2376 |
| chr4 | 681727 | 0.36% | 1552 |
| chr5 | 914805 | 0.50% | 2255 |
| chr6 | 1103987 | 0.65% | 2517 |
| chr7 | 837796 | 0.53% | 1951 |
| chr8 | 654037 | 0.45% | 1575 |
| chr9 | 638504 | 0.46% | 1557 |
| chr10 | 650540 | 0.49% | 1592 |
| chr11 | 983153 | 0.73% | 2330 |
| chr12 | 972539 | 0.73% | 2347 |
| chr13 | 354210 | 0.31% | 819 |
| chr14 | 542618 | 0.51% | 1297 |
| chr15 | 530402 | 0.52% | 1252 |
| chr16 | 672448 | 0.74% | 1633 |
| chr17 | 943100 | 1.13% | 2334 |
| chr18 | 252543 | 0.31% | 600 |
| chr19 | 1245366 | 2.12% | 3061 |
| chr20 | 528129 | 0.82% | 1288 |
| chr21 | 166810 | 0.36% | 409 |
| chr22 | 435247 | 0.86% | 1094 |
| chrX | 421226 | 0.27% | 1076 |
| chrY | 10441 | 0.02% | 28 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41877 | 1 | 6292 | 416.69 | 384 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF468LYO.bed.gz | 639.19 KB | ba4bfac04ac18497eed776496e712a6c |
| ENCFF468LYO.tabix.bed.gz | 483.4 KB | 01ee198fdaecccd867b2083a1bafac1d |
| ENCFF468LYO.tabix.bed.gz.tbi | 150.0 KB | 2fd55fd019c7da97ed2f866d723c703f |
| genomic_resource.yaml | 3.13 KB | 54e32ef55351eb90d96b900f7930f6cc |
| statistics/ |