Resource
| Id | TF_ChIP-seq/ENCSR000BST |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BST [biosample_summary="Homo sapiens MCF-7" and target="GATA3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN399CCN|/analyses/ENCAN399CCN/} has in progress subobject document {5766f25a-70bd-4152-b965-99da255de785|/documents/5766f25a-70bd-4152-b965-99da255de785/} audit_internal_action: Released analysis {ENCAN399CCN|/analyses/ENCAN399CCN/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF944GIS|/files/ENCFF944GIS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 8717931 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting GATA3-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 {ENCFF944GIS|/files/ENCFF944GIS/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF944GIS|/files/ENCFF944GIS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.91. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF565QWY|/files/ENCFF565QWY/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline have a rescue ratio of 1.35 and a self consistency ratio of 2.19. 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_ENCSR000BST | float |
TF_ChIP-seq_ENCSR000BST |
TF_ChIP-seq ENCSR000BST [biosample_summary="Homo sapiens MCF-7" and target="GATA3"]
|
 |
[4.52, 624] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 14549196 | 0.45% | 49023 |
| chr1 | 1175850 | 0.47% | 3959 |
| chr2 | 1316217 | 0.54% | 4487 |
| chr3 | 1050116 | 0.53% | 3507 |
| chr4 | 633088 | 0.33% | 2172 |
| chr5 | 959917 | 0.53% | 3180 |
| chr6 | 1014763 | 0.59% | 3437 |
| chr7 | 840754 | 0.53% | 2834 |
| chr8 | 810326 | 0.56% | 2719 |
| chr9 | 583060 | 0.42% | 1975 |
| chr10 | 812467 | 0.61% | 2739 |
| chr11 | 561269 | 0.42% | 1859 |
| chr12 | 724030 | 0.54% | 2431 |
| chr13 | 283726 | 0.25% | 951 |
| chr14 | 750000 | 0.70% | 2514 |
| chr15 | 471951 | 0.46% | 1609 |
| chr16 | 429632 | 0.48% | 1450 |
| chr17 | 540121 | 0.65% | 1818 |
| chr18 | 214082 | 0.27% | 727 |
| chr19 | 294574 | 0.50% | 981 |
| chr20 | 444493 | 0.69% | 1507 |
| chr21 | 171959 | 0.37% | 577 |
| chr22 | 173285 | 0.34% | 589 |
| chrX | 293516 | 0.19% | 1001 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 49023 | 1 | 1176 | 296.78 | 370 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF565QWY.bed.gz | 774.63 KB | e6836d1f534e7bc0aac03d710684af83 |
| ENCFF565QWY.tabix.bed.gz | 570.39 KB | 88876748831b52f57e899311a6bd751f |
| ENCFF565QWY.tabix.bed.gz.tbi | 268.78 KB | 52824a0811643a4a1348180699c671e5 |
| genomic_resource.yaml | 3.92 KB | 3812c2371d74cc39b28b3852564e1a35 |
| statistics/ |