Resource
| Id | TF_ChIP-seq/ENCSR000BGZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BGZ [biosample_summary="Homo sapiens GM12878" and target="TCF12"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF768VSH|/files/ENCFF768VSH/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN115JAP|/analyses/ENCAN115JAP/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF101LKK|/files/ENCFF101LKK/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 11256226 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TCF12-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 {ENCFF291PCM|/files/ENCFF291PCM/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13227344 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting TCF12-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 {ENCFF101LKK|/files/ENCFF101LKK/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.79. 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 {ENCFF101LKK|/files/ENCFF101LKK/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 4.63. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BGZ | float |
TF_ChIP-seq_ENCSR000BGZ |
TF_ChIP-seq ENCSR000BGZ [biosample_summary="Homo sapiens GM12878" and target="TCF12"]
|
 |
[3.74, 390] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6053817 | 0.19% | 25782 |
| chr1 | 556757 | 0.22% | 2367 |
| chr1_KI270713v1_random | 256 | 0.63% | 1 |
| chr2 | 446151 | 0.18% | 1903 |
| chr3 | 355187 | 0.18% | 1508 |
| chr4 | 212465 | 0.11% | 895 |
| chr5 | 317637 | 0.17% | 1343 |
| chr6 | 353365 | 0.21% | 1501 |
| chr7 | 282403 | 0.18% | 1197 |
| chr8 | 248519 | 0.17% | 1065 |
| chr9 | 233446 | 0.17% | 1012 |
| chr10 | 285387 | 0.21% | 1220 |
| chr11 | 307849 | 0.23% | 1304 |
| chr12 | 309787 | 0.23% | 1327 |
| chr13 | 124096 | 0.11% | 532 |
| chr14 | 209094 | 0.20% | 896 |
| chr15 | 206338 | 0.20% | 874 |
| chr16 | 266589 | 0.30% | 1134 |
| chr17 | 347359 | 0.42% | 1491 |
| chr17_GL000205v2_random | 1326 | 0.71% | 8 |
| chr18 | 112819 | 0.14% | 472 |
| chr19 | 316170 | 0.54% | 1346 |
| chr20 | 173280 | 0.27% | 741 |
| chr21 | 69222 | 0.15% | 292 |
| chr22 | 138956 | 0.27% | 587 |
| chrEBV | 46570 | 27.10% | 205 |
| chrM | 5885 | 35.52% | 23 |
| chrUn_GL000219v1 | 256 | 0.14% | 1 |
| chrX | 126648 | 0.08% | 537 |
| 3338 contigs with no values (185710574 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 25782 | 1 | 715 | 234.81 | 256 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF768VSH.bed.gz | 446.97 KB | 9edaafcabc15b0befeed308e57dffb37 |
| ENCFF768VSH.tabix.bed.gz | 297.18 KB | 743e7f1ea7ff8abdec089da3cafdd59a |
| ENCFF768VSH.tabix.bed.gz.tbi | 148.81 KB | 4420d6797c1044544037e939d682e25c |
| genomic_resource.yaml | 3.83 KB | 086f6338c330ed79e3cbb1d57a7a750f |
| statistics/ |