Resource
| Id | TF_ChIP-seq/ENCSR000ALV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000ALV [biosample_summary="Homo sapiens mammary epithelial cell female adult (50 years)" and target="CTCF"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (50 years) output_type: IDR thresholded peaks audit_error: Processed alignments file {ENCFF472NHA|/files/ENCFF472NHA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 4916002 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-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_internal_action: Released analysis {ENCAN429XCN|/analyses/ENCAN429XCN/} has in progress subobject document {52887bb2-dff6-4639-93be-2be188fc853c|/documents/52887bb2-dff6-4639-93be-2be188fc853c/} audit_internal_action: Released analysis {ENCAN429XCN|/analyses/ENCAN429XCN/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF086QJQ|/files/ENCFF086QJQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 9512981 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting CTCF-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 {ENCFF086QJQ|/files/ENCFF086QJQ/} processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF086QJQ|/files/ENCFF086QJQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.35. 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 {ENCFF472NHA|/files/ENCFF472NHA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 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 {ENCFF472NHA|/files/ENCFF472NHA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.76. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000ALV | float |
TF_ChIP-seq_ENCSR000ALV |
TF_ChIP-seq ENCSR000ALV [biosample_summary="Homo sapiens mammary epithelial cell female adult (50 years)" and target="CTCF"]
|
 |
[2.33, 230] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8698233 | 0.27% | 40234 |
| chr1 | 810524 | 0.33% | 3809 |
| chr2 | 675290 | 0.28% | 3111 |
| chr3 | 571448 | 0.29% | 2635 |
| chr4 | 437602 | 0.23% | 1994 |
| chr5 | 491479 | 0.27% | 2245 |
| chr6 | 503629 | 0.29% | 2314 |
| chr7 | 438194 | 0.27% | 2022 |
| chr8 | 400114 | 0.28% | 1833 |
| chr9 | 351912 | 0.25% | 1641 |
| chr10 | 395738 | 0.30% | 1826 |
| chr11 | 474412 | 0.35% | 2228 |
| chr12 | 435752 | 0.33% | 2041 |
| chr13 | 216092 | 0.19% | 965 |
| chr14 | 277071 | 0.26% | 1288 |
| chr15 | 273659 | 0.27% | 1276 |
| chr16 | 275871 | 0.31% | 1273 |
| chr17 | 370985 | 0.45% | 1760 |
| chr18 | 191472 | 0.24% | 881 |
| chr19 | 297106 | 0.51% | 1416 |
| chr20 | 241788 | 0.38% | 1125 |
| chr21 | 86367 | 0.18% | 391 |
| chr22 | 151469 | 0.30% | 712 |
| chrX | 330259 | 0.21% | 1448 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 40234 | 6 | 381 | 216.19 | 270 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF059YXD.bed.gz | 607.33 KB | 4203b524c4826e167130c1d0f0482a05 |
| ENCFF059YXD.tabix.bed.gz | 465.72 KB | e78486a0283671e2ea21dd61dc919800 |
| ENCFF059YXD.tabix.bed.gz.tbi | 266.68 KB | 0f05c143204181d998dcf53fa223ac1c |
| genomic_resource.yaml | 5.25 KB | 93e0e411a76be1ec78f4284a06f8ba09 |
| statistics/ |