Resource
| Id | TF_ChIP-seq/ENCSR000BGL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BGL [biosample_summary="Homo sapiens HepG2" and target="SIN3A"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN095ITQ|/analyses/ENCAN095ITQ/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_internal_action: File {ENCFF635YMI|/files/ENCFF635YMI/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_warning: Processed alignments file {ENCFF281FRR|/files/ENCFF281FRR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10369971 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting SIN3A-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 {ENCFF281FRR|/files/ENCFF281FRR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF281FRR|/files/ENCFF281FRR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.09. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF222NHS|/files/ENCFF222NHS/}, {ENCFF635YMI|/files/ENCFF635YMI/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.32 and a self consistency ratio of 6.66. According to ENCODE standards, having both rescue ratio and self consistency ratio values < 2 is recommended, but having only one of the ratio values < 2 is acceptable. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF735FHH|/files/ENCFF735FHH/}, {ENCFF025EZP|/files/ENCFF025EZP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline have a rescue ratio of 1.32 and a self consistency ratio of 6.66. According to ENCODE standards, having both rescue ratio and self consistency ratio values < 2 is recommended, but having only one of the ratio values < 2 is acceptable. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BGL | float |
TF_ChIP-seq_ENCSR000BGL |
TF_ChIP-seq ENCSR000BGL [biosample_summary="Homo sapiens HepG2" and target="SIN3A"]
|
 |
[5.78, 363] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8898683 | 0.28% | 28287 |
| chr1 | 813522 | 0.33% | 2555 |
| chr1_KI270713v1_random | 675 | 1.66% | 3 |
| chr2 | 773546 | 0.32% | 2555 |
| chr3 | 457410 | 0.23% | 1427 |
| chr4 | 266305 | 0.14% | 855 |
| chr5 | 338126 | 0.19% | 1090 |
| chr6 | 583453 | 0.34% | 1849 |
| chr7 | 352319 | 0.22% | 1141 |
| chr8 | 303109 | 0.21% | 963 |
| chr9 | 349245 | 0.25% | 1093 |
| chr10 | 353039 | 0.26% | 1114 |
| chr11 | 442830 | 0.33% | 1412 |
| chr12 | 403645 | 0.30% | 1268 |
| chr13 | 134502 | 0.12% | 423 |
| chr14 | 334497 | 0.31% | 1090 |
| chr15 | 239604 | 0.23% | 738 |
| chr16 | 524438 | 0.58% | 1706 |
| chr17 | 685591 | 0.82% | 2223 |
| chr17_GL000205v2_random | 647 | 0.35% | 3 |
| chr18 | 127090 | 0.16% | 399 |
| chr19 | 567597 | 0.97% | 1733 |
| chr20 | 433467 | 0.67% | 1401 |
| chr21 | 87470 | 0.19% | 262 |
| chr22 | 219593 | 0.43% | 657 |
| chrX | 106963 | 0.07% | 327 |
| 3341 contigs with no values (186078164 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 28287 | 2 | 436 | 314.59 | 307 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF635YMI.bed.gz | 402.55 KB | cc228b7f113019a06503b2dc60844057 |
| ENCFF635YMI.tabix.bed.gz | 319.26 KB | b081613444aff9c10d83c8bd29064e60 |
| ENCFF635YMI.tabix.bed.gz.tbi | 111.46 KB | e9b1dc53b2faa1bf469cca4d93768eed |
| genomic_resource.yaml | 4.46 KB | 07e2f95e4a48fcf00e75b49f85e881e5 |
| statistics/ |