Resource
| Id | TF_ChIP-seq/ENCSR000BQB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BQB [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn" and target="POLR2A"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: newborn output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN143IAM|/analyses/ENCAN143IAM/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF095RWQ|/files/ENCFF095RWQ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 10054009 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting POLR2A-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 {ENCFF095RWQ|/files/ENCFF095RWQ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF095RWQ|/files/ENCFF095RWQ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.78. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BQB | float |
TF_ChIP-seq_ENCSR000BQB |
TF_ChIP-seq ENCSR000BQB [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn" and target="POLR2A"]
|
 |
[8.31, 493] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 13012570 | 0.40% | 36220 |
| chr1 | 1322382 | 0.53% | 3771 |
| chr2 | 986002 | 0.41% | 2804 |
| chr3 | 844134 | 0.43% | 2308 |
| chr4 | 480178 | 0.25% | 1261 |
| chr5 | 602828 | 0.33% | 1702 |
| chr6 | 749025 | 0.44% | 2075 |
| chr7 | 597143 | 0.37% | 1622 |
| chr8 | 437041 | 0.30% | 1173 |
| chr9 | 547348 | 0.40% | 1520 |
| chr10 | 523164 | 0.39% | 1382 |
| chr11 | 866885 | 0.64% | 2493 |
| chr12 | 817092 | 0.61% | 2292 |
| chr13 | 228556 | 0.20% | 616 |
| chr14 | 394238 | 0.37% | 1102 |
| chr15 | 417966 | 0.41% | 1120 |
| chr16 | 500284 | 0.55% | 1403 |
| chr17 | 733353 | 0.88% | 2068 |
| chr18 | 193982 | 0.24% | 533 |
| chr19 | 749679 | 1.28% | 2155 |
| chr20 | 373466 | 0.58% | 1065 |
| chr21 | 120890 | 0.26% | 324 |
| chr22 | 287886 | 0.57% | 800 |
| chrX | 237440 | 0.15% | 628 |
| chrY | 1608 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 36220 | 1 | 11396 | 359.26 | 331 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF876VZQ.bed.gz | 491.94 KB | 701ca68b5efae47fa8d14458cd27fdf3 |
| ENCFF876VZQ.tabix.bed.gz | 413.42 KB | aa236c665b391584e7b744666a5ee1bd |
| ENCFF876VZQ.tabix.bed.gz.tbi | 135.52 KB | 5a6da8e444209e69358718e42ecf4d17 |
| genomic_resource.yaml | 3.35 KB | 2b4f287bf39801ff5c82124d0997fd88 |
| statistics/ |