Resource
| Id | TF_ChIP-seq/ENCSR000BTG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BTG [biosample_summary="Homo sapiens SK-N-SH" and target="GABPA"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN697ZWB|/analyses/ENCAN697ZWB/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF855MYB|/files/ENCFF855MYB/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline has 18356486 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting GABPA-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 {ENCFF605EBG|/files/ENCFF605EBG/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF605EBG|/files/ENCFF605EBG/} processed by ChIP-seq ENCODE4 v1.4.0 GRCh38 pipeline was generated from a library with PBC2 value of 6.24. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BTG | float |
TF_ChIP-seq_ENCSR000BTG |
TF_ChIP-seq ENCSR000BTG [biosample_summary="Homo sapiens SK-N-SH" and target="GABPA"]
|
 |
[5.46, 765] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4136220 | 0.13% | 12466 |
| chr1 | 406125 | 0.16% | 1259 |
| chr2 | 317351 | 0.13% | 960 |
| chr3 | 237445 | 0.12% | 719 |
| chr4 | 151059 | 0.08% | 456 |
| chr5 | 197926 | 0.11% | 593 |
| chr6 | 215426 | 0.13% | 652 |
| chr7 | 260285 | 0.16% | 777 |
| chr8 | 148356 | 0.10% | 430 |
| chr9 | 155846 | 0.11% | 474 |
| chr10 | 160041 | 0.12% | 481 |
| chr11 | 222171 | 0.16% | 665 |
| chr12 | 227300 | 0.17% | 683 |
| chr13 | 84339 | 0.07% | 258 |
| chr14 | 114135 | 0.11% | 338 |
| chr15 | 122279 | 0.12% | 370 |
| chr16 | 165406 | 0.18% | 504 |
| chr17 | 263437 | 0.32% | 791 |
| chr18 | 61799 | 0.08% | 194 |
| chr19 | 295117 | 0.50% | 871 |
| chr20 | 111784 | 0.17% | 326 |
| chr21 | 36072 | 0.08% | 103 |
| chr22 | 80791 | 0.16% | 243 |
| chrX | 101730 | 0.07% | 319 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 12466 | 2 | 1217 | 331.8 | 400 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF157KZY.bed.gz | 213.18 KB | 1a704340beb7c042fc96e6ea98970855 |
| ENCFF157KZY.tabix.bed.gz | 148.19 KB | a949a2ab71feb70414dd354b6656c73d |
| ENCFF157KZY.tabix.bed.gz.tbi | 89.62 KB | 9666c11351ccd2550be7171827c9e1e0 |
| genomic_resource.yaml | 3.16 KB | 37df901ebf2d9cfefa30ad8a3464798b |
| statistics/ |