Resource
| Id | Histone_ChIP-seq/ENCSR718BTD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR718BTD [biosample_summary="Homo sapiens vagina tissue female adult (53 years)" and target="H3K27ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (53 years) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN429GHO|/analyses/ENCAN429GHO/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF834JHG|/files/ENCFF834JHG/} processed by ChIP-seq ENCODE3 hg19 pipeline has 8710892 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 {ENCFF542EXN|/files/ENCFF542EXN/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF542EXN|/files/ENCFF542EXN/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.94. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR718BTD | float |
Histone_ChIP-seq_ENCSR718BTD |
Histone_ChIP-seq ENCSR718BTD [biosample_summary="Homo sapiens vagina tissue female adult (53 years)" and target="H3K27ac"]
|
 |
[1.4, 79.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 112764168 | 3.50% | 105669 |
| chr1 | 11489444 | 4.62% | 10196 |
| chr2 | 8667646 | 3.58% | 8267 |
| chr3 | 6676692 | 3.37% | 6587 |
| chr4 | 3955556 | 2.08% | 4187 |
| chr5 | 5336329 | 2.94% | 5361 |
| chr6 | 5598367 | 3.28% | 5749 |
| chr7 | 4957664 | 3.11% | 5001 |
| chr8 | 4562473 | 3.14% | 4632 |
| chr9 | 5474524 | 3.96% | 5082 |
| chr10 | 6146102 | 4.59% | 5822 |
| chr11 | 6277841 | 4.65% | 5304 |
| chr12 | 5861265 | 4.40% | 5492 |
| chr13 | 2394220 | 2.09% | 2487 |
| chr14 | 3864519 | 3.61% | 3442 |
| chr15 | 4202528 | 4.12% | 4069 |
| chr16 | 4197672 | 4.65% | 3802 |
| chr17 | 6351829 | 7.63% | 5255 |
| chr18 | 2204643 | 2.74% | 2227 |
| chr19 | 4764736 | 8.13% | 3715 |
| chr20 | 3267297 | 5.07% | 3002 |
| chr21 | 1412322 | 3.02% | 1393 |
| chr22 | 2892840 | 5.69% | 2350 |
| chrX | 2207315 | 1.41% | 2246 |
| chrY | 344 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 105669 | 185 | 34808 | 1067.15 | 671 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF829ZKD.bed.gz | 2.49 MB | d321ae53e3cdf25812c4d523ce079af6 |
| ENCFF829ZKD.tabix.bed.gz | 1.11 MB | bb45575f7e9c10869933a92c571bd084 |
| ENCFF829ZKD.tabix.bed.gz.tbi | 277.36 KB | 578d58f07a8013cfc19c81cc3af6d857 |
| genomic_resource.yaml | 3.33 KB | b5acaedc2ce838fd02df772068b78373 |
| statistics/ |