Resource
| Id | TF_ChIP-seq/ENCSR000BMR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BMR [biosample_summary="Homo sapiens K562" and target="POLR2A"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF182YZG|/files/ENCFF182YZG/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN370MHQ|/analyses/ENCAN370MHQ/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF140UJB|/files/ENCFF140UJB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19584370 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 {ENCFF140UJB|/files/ENCFF140UJB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF140UJB|/files/ENCFF140UJB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.44. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BMR | float |
TF_ChIP-seq_ENCSR000BMR |
TF_ChIP-seq ENCSR000BMR [biosample_summary="Homo sapiens K562" and target="POLR2A"]
|
 |
[8.79, 536] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 15726483 | 0.49% | 41805 |
| chr1 | 1838491 | 0.74% | 4801 |
| chr1_KI270713v1_random | 530 | 1.30% | 1 |
| chr1_KI270714v1_random | 530 | 1.27% | 1 |
| chr2 | 894121 | 0.37% | 2341 |
| chr3 | 823418 | 0.42% | 2114 |
| chr4 | 489090 | 0.26% | 1291 |
| chr5 | 661263 | 0.36% | 1707 |
| chr6 | 1098891 | 0.64% | 2722 |
| chr7 | 892844 | 0.56% | 2279 |
| chr8 | 506995 | 0.35% | 1326 |
| chr9 | 609673 | 0.44% | 1629 |
| chr10 | 563010 | 0.42% | 1508 |
| chr11 | 892325 | 0.66% | 2404 |
| chr12 | 767276 | 0.58% | 2107 |
| chr13 | 160078 | 0.14% | 470 |
| chr14 | 327428 | 0.31% | 918 |
| chr15 | 432995 | 0.42% | 1144 |
| chr16 | 796744 | 0.88% | 2198 |
| chr17 | 1020349 | 1.23% | 2751 |
| chr17_GL000205v2_random | 530 | 0.29% | 1 |
| chr18 | 187946 | 0.23% | 488 |
| chr19 | 1336066 | 2.28% | 3675 |
| chr20 | 456655 | 0.71% | 1259 |
| chr21 | 194120 | 0.42% | 498 |
| chr22 | 408911 | 0.80% | 1132 |
| chrUn_GL000219v1 | 731 | 0.41% | 3 |
| chrUn_KI270750v1 | 530 | 0.36% | 1 |
| chrX | 364943 | 0.23% | 1036 |
| 3338 contigs with no values (185708399 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41805 | 1 | 9219 | 376.19 | 352 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF182YZG.bed.gz | 649.3 KB | b944c338bd7ff9253c3498707b9b6b12 |
| ENCFF182YZG.tabix.bed.gz | 485.25 KB | 60adab9115e9dcfd53b492c966a4648c |
| ENCFF182YZG.tabix.bed.gz.tbi | 144.37 KB | c6699016bd1ba4c370f85bf52ae963e9 |
| genomic_resource.yaml | 3.33 KB | 9d7275e0e4c5bd7684091ca7f37a84c8 |
| statistics/ |