Resource
| Id | TF_ChIP-seq/ENCSR000BSM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BSM [biosample_summary="Homo sapiens SK-N-SH" and target="YY1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN626IKY|/analyses/ENCAN626IKY/} has in progress subobject document {66b9e2c9-89c9-4f73-a5b7-bdf7c6f90333|/documents/66b9e2c9-89c9-4f73-a5b7-bdf7c6f90333/} audit_internal_action: Released analysis {ENCAN626IKY|/analyses/ENCAN626IKY/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF804ZFN|/files/ENCFF804ZFN/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline has 10645779 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting YY1-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 {ENCFF804ZFN|/files/ENCFF804ZFN/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF804ZFN|/files/ENCFF804ZFN/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC2 value of 7.93. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BSM | float |
TF_ChIP-seq_ENCSR000BSM |
TF_ChIP-seq ENCSR000BSM [biosample_summary="Homo sapiens SK-N-SH" and target="YY1"]
|
 |
[4.88, 645] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6328040 | 0.20% | 18243 |
| chr1 | 604453 | 0.24% | 1793 |
| chr2 | 506185 | 0.21% | 1393 |
| chr3 | 385083 | 0.19% | 1120 |
| chr4 | 257013 | 0.14% | 733 |
| chr5 | 373590 | 0.21% | 1090 |
| chr6 | 357915 | 0.21% | 1022 |
| chr7 | 468343 | 0.29% | 1348 |
| chr8 | 234546 | 0.16% | 671 |
| chr9 | 239357 | 0.17% | 674 |
| chr10 | 286354 | 0.21% | 834 |
| chr11 | 321917 | 0.24% | 938 |
| chr12 | 343799 | 0.26% | 992 |
| chr13 | 117121 | 0.10% | 333 |
| chr14 | 189326 | 0.18% | 566 |
| chr15 | 198458 | 0.19% | 582 |
| chr16 | 200836 | 0.22% | 579 |
| chr17 | 380488 | 0.46% | 1082 |
| chr18 | 108087 | 0.13% | 314 |
| chr19 | 302270 | 0.52% | 876 |
| chr20 | 145086 | 0.23% | 399 |
| chr21 | 54549 | 0.12% | 161 |
| chr22 | 96317 | 0.19% | 263 |
| chrX | 156947 | 0.10% | 480 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 18243 | 1 | 1756 | 346.87 | 380 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF042OEY.bed.gz | 278.73 KB | c2c627fbab6bac4ce349e6d39a7f7096 |
| ENCFF042OEY.tabix.bed.gz | 211.92 KB | eb83ba635fc05e04318343b3e79e1480 |
| ENCFF042OEY.tabix.bed.gz.tbi | 108.22 KB | f8123d0622adbaed7c85e944ada74f7b |
| genomic_resource.yaml | 3.38 KB | fcac0defb0f45608b0e08ead79d9c792 |
| statistics/ |