Resource
| Id | TF_ChIP-seq/ENCSR000BIS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BIS [biosample_summary="Homo sapiens H1" and target="SIN3A"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN729GRC|/analyses/ENCAN729GRC/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF036SLY|/files/ENCFF036SLY/} processed by ChIP-seq ENCODE3 hg19 pipeline has 11065222 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: Processed alignments file {ENCFF655DGW|/files/ENCFF655DGW/} processed by ChIP-seq ENCODE3 hg19 pipeline has 14035468 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 {ENCFF655DGW|/files/ENCFF655DGW/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF655DGW|/files/ENCFF655DGW/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.12. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BIS | float |
TF_ChIP-seq_ENCSR000BIS |
TF_ChIP-seq ENCSR000BIS [biosample_summary="Homo sapiens H1" and target="SIN3A"]
|
 |
[4.32, 390] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4210046 | 0.13% | 15522 |
| chr1 | 442923 | 0.18% | 1625 |
| chr2 | 257721 | 0.11% | 941 |
| chr3 | 241542 | 0.12% | 885 |
| chr4 | 160922 | 0.08% | 586 |
| chr5 | 196170 | 0.11% | 723 |
| chr6 | 258652 | 0.15% | 958 |
| chr7 | 189998 | 0.12% | 708 |
| chr8 | 156536 | 0.11% | 575 |
| chr9 | 169637 | 0.12% | 625 |
| chr10 | 178248 | 0.13% | 672 |
| chr11 | 252794 | 0.19% | 941 |
| chr12 | 234424 | 0.18% | 875 |
| chr13 | 82566 | 0.07% | 293 |
| chr14 | 143010 | 0.13% | 522 |
| chr15 | 153252 | 0.15% | 567 |
| chr16 | 180400 | 0.20% | 672 |
| chr17 | 254279 | 0.31% | 939 |
| chr18 | 65796 | 0.08% | 239 |
| chr19 | 294758 | 0.50% | 1092 |
| chr20 | 132058 | 0.20% | 496 |
| chr21 | 28123 | 0.06% | 103 |
| chr22 | 89289 | 0.18% | 317 |
| chrX | 46638 | 0.03% | 167 |
| chrY | 310 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 15522 | 1 | 398 | 271.23 | 310 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF820OMK.bed.gz | 249.91 KB | 23a7613b25af81f5dbf2037400bca991 |
| ENCFF820OMK.tabix.bed.gz | 177.92 KB | 92baae51a474b7d80ea12250dcba4990 |
| ENCFF820OMK.tabix.bed.gz.tbi | 94.25 KB | 7676d5402e825e941f4f216d46a6de02 |
| genomic_resource.yaml | 3.62 KB | bdcda30faa3fadb7a8187e6cbebece94 |
| statistics/ |