Resource
| Id | Histone_ChIP-seq/ENCSR002YRE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR002YRE [biosample_summary="Homo sapiens IMR-90" and target="H3K27ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN781CQQ|/analyses/ENCAN781CQQ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF071VOI|/files/ENCFF071VOI/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 8958790 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27ac-human and investigated as a narrow histone mark 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 {ENCFF146UYU|/files/ENCFF146UYU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR002YRE | float |
Histone_ChIP-seq_ENCSR002YRE |
Histone_ChIP-seq ENCSR002YRE [biosample_summary="Homo sapiens IMR-90" and target="H3K27ac"]
|
 |
[1.59, 41] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 50154829 | 1.56% | 117855 |
| chr1 | 4506815 | 1.81% | 10443 |
| chr1_KI270713v1_random | 134 | 0.33% | 1 |
| chr2 | 4408494 | 1.82% | 10682 |
| chr3 | 3057552 | 1.54% | 7562 |
| chr4 | 2085617 | 1.10% | 5473 |
| chr5 | 2856559 | 1.57% | 6837 |
| chr6 | 2803286 | 1.64% | 6903 |
| chr7 | 2352466 | 1.48% | 5648 |
| chr8 | 2203379 | 1.52% | 5517 |
| chr9 | 2336484 | 1.69% | 5332 |
| chr10 | 2261519 | 1.69% | 5391 |
| chr11 | 2922494 | 2.16% | 6488 |
| chr12 | 2545101 | 1.91% | 5912 |
| chr13 | 1252241 | 1.09% | 3204 |
| chr14 | 1583673 | 1.48% | 3710 |
| chr15 | 1888260 | 1.85% | 4373 |
| chr16 | 1812060 | 2.01% | 3855 |
| chr17 | 2560425 | 3.08% | 5170 |
| chr17_GL000205v2_random | 471 | 0.25% | 2 |
| chr18 | 968343 | 1.20% | 2490 |
| chr19 | 1790381 | 3.05% | 3615 |
| chr20 | 1256811 | 1.95% | 2899 |
| chr21 | 640897 | 1.37% | 1534 |
| chr22 | 1053120 | 2.07% | 2243 |
| chrUn_GL000195v1 | 528 | 0.29% | 3 |
| chrUn_GL000219v1 | 1113 | 0.62% | 3 |
| chrUn_GL000220v1 | 211 | 0.13% | 1 |
| chrX | 1006395 | 0.64% | 2564 |
| 3338 contigs with no values (185554268 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 117855 | 125 | 12333 | 425.56 | 291 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF730BVO.bed.gz | 2.91 MB | 568f9b5d553717209d81b8cd1faf8369 |
| ENCFF730BVO.tabix.bed.gz | 1.23 MB | 7c6293ffdb2ba9505b44a7de2a5d1c09 |
| ENCFF730BVO.tabix.bed.gz.tbi | 273.83 KB | 58fed11f4e28443d566ceb981dad9b9b |
| genomic_resource.yaml | 2.53 KB | bf8714a38a32ce98bab45e0ed105e891 |
| statistics/ |