Resource
| Id | TF_ChIP-seq/ENCSR000BPL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BPL [biosample_summary="Homo sapiens SK-N-MC" and target="POLR2AphosphoS5"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN670HFU|/analyses/ENCAN670HFU/} has in progress subobject document {a37a6b7b-9f46-4907-adf2-e9d42e99510c|/documents/a37a6b7b-9f46-4907-adf2-e9d42e99510c/} audit_internal_action: Released analysis {ENCAN670HFU|/analyses/ENCAN670HFU/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF830JTI|/files/ENCFF830JTI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 14240675 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting POLR2AphosphoS5-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 {ENCFF854PCK|/files/ENCFF854PCK/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 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 {ENCFF854PCK|/files/ENCFF854PCK/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.54. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF638SXR|/files/ENCFF638SXR/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 2.15 and a self consistency ratio of 1.05. 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_ENCSR000BPL | float |
TF_ChIP-seq_ENCSR000BPL |
TF_ChIP-seq ENCSR000BPL [biosample_summary="Homo sapiens SK-N-MC" and target="POLR2AphosphoS5"]
|
 |
[7.88, 536] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11840440 | 0.37% | 34549 |
| chr1 | 1198177 | 0.48% | 3526 |
| chr2 | 856860 | 0.35% | 2464 |
| chr3 | 747803 | 0.38% | 2127 |
| chr4 | 526181 | 0.28% | 1475 |
| chr5 | 620740 | 0.34% | 1769 |
| chr6 | 962538 | 0.56% | 2698 |
| chr7 | 580970 | 0.36% | 1684 |
| chr8 | 789898 | 0.54% | 2225 |
| chr9 | 449942 | 0.33% | 1311 |
| chr10 | 249080 | 0.19% | 751 |
| chr11 | 585901 | 0.43% | 1747 |
| chr12 | 630089 | 0.47% | 1818 |
| chr13 | 314300 | 0.27% | 910 |
| chr14 | 412211 | 0.39% | 1208 |
| chr15 | 323075 | 0.32% | 948 |
| chr16 | 302711 | 0.34% | 925 |
| chr17 | 540304 | 0.65% | 1653 |
| chr18 | 191969 | 0.24% | 560 |
| chr19 | 690183 | 1.18% | 2155 |
| chr20 | 325071 | 0.50% | 937 |
| chr21 | 83306 | 0.18% | 248 |
| chr22 | 202290 | 0.40% | 616 |
| chrX | 256841 | 0.16% | 794 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 34549 | 1 | 3585 | 342.71 | 328 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF638SXR.bed.gz | 528.63 KB | 816c44349ee70754d890a33e75d9f9cd |
| ENCFF638SXR.tabix.bed.gz | 400.05 KB | 04f5a247a78e84250a9816eae5c0b277 |
| ENCFF638SXR.tabix.bed.gz.tbi | 160.38 KB | b0051e78b9d1b27b63d44476c5cde73a |
| genomic_resource.yaml | 4.26 KB | ec93143689d9ae5daff4f09463c007a5 |
| statistics/ |