Resource
| Id | TF_ChIP-seq/ENCSR000BGM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BGM [biosample_summary="Homo sapiens HepG2" and target="USF1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF914IFQ|/files/ENCFF914IFQ/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN117NQJ|/analyses/ENCAN117NQJ/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF582CJF|/files/ENCFF582CJF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 12638677 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting USF1-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 {ENCFF582CJF|/files/ENCFF582CJF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF582CJF|/files/ENCFF582CJF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.33. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF498RHX|/files/ENCFF498RHX/}, {ENCFF586WRZ|/files/ENCFF586WRZ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.25 and a self consistency ratio of 2.35. 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: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF895AOF|/files/ENCFF895AOF/}, {ENCFF914IFQ|/files/ENCFF914IFQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.25 and a self consistency ratio of 2.35. 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. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BGM | float |
TF_ChIP-seq_ENCSR000BGM |
TF_ChIP-seq ENCSR000BGM [biosample_summary="Homo sapiens HepG2" and target="USF1"]
|
 |
[4.44, 414] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4602380 | 0.14% | 24132 |
| chr1 | 401192 | 0.16% | 2107 |
| chr1_KI270713v1_random | 200 | 0.49% | 1 |
| chr2 | 450118 | 0.19% | 2355 |
| chr3 | 232356 | 0.12% | 1216 |
| chr4 | 143579 | 0.08% | 757 |
| chr5 | 183385 | 0.10% | 963 |
| chr6 | 259084 | 0.15% | 1358 |
| chr7 | 197430 | 0.12% | 1041 |
| chr8 | 165101 | 0.11% | 862 |
| chr9 | 191290 | 0.14% | 1009 |
| chr10 | 189097 | 0.14% | 989 |
| chr11 | 199726 | 0.15% | 1046 |
| chr12 | 205509 | 0.15% | 1074 |
| chr13 | 78792 | 0.07% | 410 |
| chr14 | 167354 | 0.16% | 879 |
| chr15 | 118606 | 0.12% | 618 |
| chr16 | 284117 | 0.31% | 1489 |
| chr17 | 308734 | 0.37% | 1616 |
| chr17_GL000205v2_random | 600 | 0.32% | 3 |
| chr18 | 76980 | 0.10% | 403 |
| chr19 | 224517 | 0.38% | 1183 |
| chr20 | 272044 | 0.42% | 1425 |
| chr21 | 54043 | 0.12% | 282 |
| chr22 | 123986 | 0.24% | 653 |
| chrUn_GL000195v1 | 200 | 0.11% | 1 |
| chrX | 73740 | 0.05% | 389 |
| chrY | 600 | <0.01% | 3 |
| 3339 contigs with no values (128667853 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 24132 | 1 | 592 | 190.72 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF914IFQ.bed.gz | 386.59 KB | 17a74daeb420617d9eecadc51715cc37 |
| ENCFF914IFQ.tabix.bed.gz | 281.22 KB | 7e8b80626be0fcba1424e4383e2c331e |
| ENCFF914IFQ.tabix.bed.gz.tbi | 160.57 KB | 5a8691506357606d8805fc63185e8bd2 |
| genomic_resource.yaml | 4.46 KB | 95701542de26fa74ff4d56b29633b8bd |
| statistics/ |