Resource
| Id | TF_ChIP-seq/ENCSR000BNP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BNP [biosample_summary="Homo sapiens GM12878" and target="YY1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN785XYH|/analyses/ENCAN785XYH/} has in progress subobject document {7dd7c605-dd9a-470a-8dd4-5ca735baca0f|/documents/7dd7c605-dd9a-470a-8dd4-5ca735baca0f/} audit_internal_action: Released analysis {ENCAN785XYH|/analyses/ENCAN785XYH/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF676OVC|/files/ENCFF676OVC/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 14333464 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: Processed alignments file {ENCFF481OXC|/files/ENCFF481OXC/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 16919080 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 {ENCFF676OVC|/files/ENCFF676OVC/} 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 {ENCFF676OVC|/files/ENCFF676OVC/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.21. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BNP | float |
TF_ChIP-seq_ENCSR000BNP |
TF_ChIP-seq ENCSR000BNP [biosample_summary="Homo sapiens GM12878" and target="YY1"]
|
 |
[4.79, 511] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10907575 | 0.34% | 39144 |
| chr1 | 1047485 | 0.42% | 3747 |
| chr2 | 782989 | 0.32% | 2799 |
| chr3 | 648596 | 0.33% | 2298 |
| chr4 | 409301 | 0.22% | 1453 |
| chr5 | 571525 | 0.31% | 2028 |
| chr6 | 672292 | 0.39% | 2458 |
| chr7 | 502047 | 0.32% | 1787 |
| chr8 | 411391 | 0.28% | 1472 |
| chr9 | 429671 | 0.31% | 1556 |
| chr10 | 478768 | 0.36% | 1741 |
| chr11 | 567123 | 0.42% | 2031 |
| chr12 | 596380 | 0.45% | 2146 |
| chr13 | 206021 | 0.18% | 744 |
| chr14 | 373339 | 0.35% | 1334 |
| chr15 | 364337 | 0.36% | 1316 |
| chr16 | 449596 | 0.50% | 1620 |
| chr17 | 608738 | 0.73% | 2218 |
| chr18 | 205950 | 0.26% | 743 |
| chr19 | 639854 | 1.09% | 2309 |
| chr20 | 311169 | 0.48% | 1117 |
| chr21 | 105931 | 0.23% | 381 |
| chr22 | 255396 | 0.50% | 913 |
| chrX | 269676 | 0.17% | 933 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 39144 | 1 | 1597 | 278.65 | 344 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF446ZSX.bed.gz | 599.8 KB | 6942c2126255ef3a76a197ec93a3459e |
| ENCFF446ZSX.tabix.bed.gz | 451.76 KB | 8b7665c7df7d807e0a81d19001858399 |
| ENCFF446ZSX.tabix.bed.gz.tbi | 204.14 KB | cb1133c6f0814519ff67f21b1caa9ecc |
| genomic_resource.yaml | 3.87 KB | 45747ea2890062764a11dd56418b42ef |
| statistics/ |