Resource
| Id | TF_ChIP-seq/ENCSR000BTD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BTD [biosample_summary="Homo sapiens Ishikawa" and target="SRF"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN299YOS|/analyses/ENCAN299YOS/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_internal_action: Released analysis {ENCAN299YOS|/analyses/ENCAN299YOS/} has in progress subobject document {59226277-5032-48ea-b774-d041cbd32d40|/documents/59226277-5032-48ea-b774-d041cbd32d40/} audit_warning: Processed alignments file {ENCFF562OZO|/files/ENCFF562OZO/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 18752640 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting SRF-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 {ENCFF714RQM|/files/ENCFF714RQM/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.30 and a self consistency ratio of 2.34. 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_ENCSR000BTD | float |
TF_ChIP-seq_ENCSR000BTD |
TF_ChIP-seq ENCSR000BTD [biosample_summary="Homo sapiens Ishikawa" and target="SRF"]
|
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[5.76, 675] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 3719302 | 0.12% | 13808 |
| chr1 | 354430 | 0.14% | 1333 |
| chr2 | 258496 | 0.11% | 968 |
| chr3 | 234385 | 0.12% | 866 |
| chr4 | 178414 | 0.09% | 661 |
| chr5 | 177227 | 0.10% | 646 |
| chr6 | 194030 | 0.11% | 721 |
| chr7 | 175146 | 0.11% | 643 |
| chr8 | 142047 | 0.10% | 522 |
| chr9 | 158726 | 0.11% | 593 |
| chr10 | 198678 | 0.15% | 730 |
| chr11 | 179743 | 0.13% | 660 |
| chr12 | 259926 | 0.20% | 971 |
| chr13 | 79944 | 0.07% | 301 |
| chr14 | 124534 | 0.12% | 469 |
| chr15 | 111150 | 0.11% | 410 |
| chr16 | 147833 | 0.16% | 553 |
| chr17 | 207524 | 0.25% | 754 |
| chr18 | 72288 | 0.09% | 280 |
| chr19 | 216086 | 0.37% | 799 |
| chr20 | 95597 | 0.15% | 362 |
| chr21 | 29497 | 0.06% | 111 |
| chr22 | 82911 | 0.16% | 300 |
| chrX | 40690 | 0.03% | 155 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 13808 | 2 | 672 | 269.36 | 304 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF714RQM.bed.gz | 223.25 KB | f72872826bfe9038cf061ab2509d3700 |
| ENCFF714RQM.tabix.bed.gz | 161.5 KB | b726b3e2b185b00c19fa08d696ff102a |
| ENCFF714RQM.tabix.bed.gz.tbi | 101.17 KB | 3b22f7be106f753388041a36a1df51be |
| genomic_resource.yaml | 2.6 KB | 38655408018bf1ddc8c8937c8f8379ec |
| statistics/ |
