Resource
| Id | TF_ChIP-seq/ENCSR000BSU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BSU [biosample_summary="Homo sapiens MCF-7" and target="JUND"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN660DIM|/analyses/ENCAN660DIM/} has in progress subobject document {e82fcdb1-8dec-433c-bca8-24fac5136dbb|/documents/e82fcdb1-8dec-433c-bca8-24fac5136dbb/} audit_internal_action: Released analysis {ENCAN660DIM|/analyses/ENCAN660DIM/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_warning: Processed alignments file {ENCFF065JCY|/files/ENCFF065JCY/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 13135800 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting JUND-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 {ENCFF708XQE|/files/ENCFF708XQE/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 16188711 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting JUND-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 {ENCFF065JCY|/files/ENCFF065JCY/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF065JCY|/files/ENCFF065JCY/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.40. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BSU | float |
TF_ChIP-seq_ENCSR000BSU |
TF_ChIP-seq ENCSR000BSU [biosample_summary="Homo sapiens MCF-7" and target="JUND"]
|
 |
[4.16, 466] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5060465 | 0.16% | 15411 |
| chr1 | 412899 | 0.17% | 1263 |
| chr2 | 447835 | 0.18% | 1353 |
| chr3 | 340975 | 0.17% | 1015 |
| chr4 | 144371 | 0.08% | 409 |
| chr5 | 301025 | 0.17% | 896 |
| chr6 | 327610 | 0.19% | 983 |
| chr7 | 305636 | 0.19% | 946 |
| chr8 | 297599 | 0.21% | 955 |
| chr9 | 218878 | 0.16% | 657 |
| chr10 | 275002 | 0.21% | 827 |
| chr11 | 193000 | 0.14% | 565 |
| chr12 | 254033 | 0.19% | 779 |
| chr13 | 69311 | 0.06% | 203 |
| chr14 | 287489 | 0.27% | 910 |
| chr15 | 160230 | 0.16% | 497 |
| chr16 | 201755 | 0.22% | 625 |
| chr17 | 235255 | 0.28% | 739 |
| chr18 | 58617 | 0.07% | 171 |
| chr19 | 120693 | 0.21% | 357 |
| chr20 | 214411 | 0.33% | 689 |
| chr21 | 63619 | 0.14% | 185 |
| chr22 | 63947 | 0.13% | 193 |
| chrX | 66275 | 0.04% | 194 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 15411 | 4 | 553 | 328.37 | 400 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF398OOD.bed.gz | 243.32 KB | 0639bb526625bea147eeeddbdee80f7a |
| ENCFF398OOD.tabix.bed.gz | 178.97 KB | 17794971d3f6759d453c76d764e30c34 |
| ENCFF398OOD.tabix.bed.gz.tbi | 100.68 KB | 5bc6902bc53ddf2a05590790c4d85990 |
| genomic_resource.yaml | 3.87 KB | 70b0f901e01dd46a5130bb1783322ef3 |
| statistics/ |