Resource
| Id | TF_ChIP-seq/ENCSR000BJA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BJA [biosample_summary="Homo sapiens H1" and target="EGR1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF477ANT|/files/ENCFF477ANT/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN287KFQ|/analyses/ENCAN287KFQ/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF777MZR|/files/ENCFF777MZR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17905180 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting EGR1-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: Processed alignments file {ENCFF054DVF|/files/ENCFF054DVF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19044316 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting EGR1-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: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF004MNA|/files/ENCFF004MNA/}, {ENCFF477ANT|/files/ENCFF477ANT/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.28 and a self consistency ratio of 2.46. 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 {ENCFF469MQG|/files/ENCFF469MQG/}, {ENCFF042WRS|/files/ENCFF042WRS/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.28 and a self consistency ratio of 2.46. 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_ENCSR000BJA | float |
TF_ChIP-seq_ENCSR000BJA |
TF_ChIP-seq ENCSR000BJA [biosample_summary="Homo sapiens H1" and target="EGR1"]
|
 |
[5.47, 466] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 3069926 | 0.10% | 12036 |
| chr1 | 310558 | 0.12% | 1219 |
| chr1_KI270713v1_random | 264 | 0.65% | 1 |
| chr2 | 215074 | 0.09% | 839 |
| chr3 | 168150 | 0.08% | 656 |
| chr4 | 118328 | 0.06% | 461 |
| chr5 | 155332 | 0.09% | 609 |
| chr6 | 171300 | 0.10% | 676 |
| chr7 | 161141 | 0.10% | 631 |
| chr8 | 124792 | 0.09% | 495 |
| chr9 | 127317 | 0.09% | 498 |
| chr10 | 130808 | 0.10% | 511 |
| chr11 | 166180 | 0.12% | 647 |
| chr12 | 171147 | 0.13% | 669 |
| chr13 | 66409 | 0.06% | 261 |
| chr14 | 93392 | 0.09% | 365 |
| chr15 | 95458 | 0.09% | 374 |
| chr16 | 128512 | 0.14% | 503 |
| chr17 | 188241 | 0.23% | 738 |
| chr18 | 49599 | 0.06% | 193 |
| chr19 | 196545 | 0.34% | 772 |
| chr20 | 89320 | 0.14% | 352 |
| chr21 | 28277 | 0.06% | 115 |
| chr22 | 65322 | 0.13% | 256 |
| chrM | 6684 | 40.34% | 29 |
| chrUn_KI270466v1 | 264 | 21.41% | 1 |
| chrUn_KI270467v1 | 528 | 13.47% | 2 |
| chrX | 40984 | 0.03% | 163 |
| 3339 contigs with no values (186242033 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 12036 | 5 | 290 | 255.06 | 264 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF477ANT.bed.gz | 200.72 KB | 29679d804ec39d878f61ec037a69b2b7 |
| ENCFF477ANT.tabix.bed.gz | 140.57 KB | 56fc851d41a16b46a67aa35fe1169b3a |
| ENCFF477ANT.tabix.bed.gz.tbi | 91.7 KB | 1bc7d36dfde3d9997ee96d0cf9e6a7e7 |
| genomic_resource.yaml | 3.64 KB | cc179a318a0320d3d5aa5588a0ccc562 |
| statistics/ |