Resource
| Id | Histone_ChIP-seq/ENCSR522EGW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR522EGW [biosample_summary="Homo sapiens B cell" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN817TRL|/analyses/ENCAN817TRL/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF123SLZ|/files/ENCFF123SLZ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 8965445 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_not_compliant: Processed alignments file {ENCFF302OGB|/files/ENCFF302OGB/} processed by ChIP-seq ENCODE3 hg19 pipeline has 8176357 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 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 {ENCFF302OGB|/files/ENCFF302OGB/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF302OGB|/files/ENCFF302OGB/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.62. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR522EGW | float |
Histone_ChIP-seq_ENCSR522EGW |
Histone_ChIP-seq ENCSR522EGW [biosample_summary="Homo sapiens B cell" and target="H3K27me3"]
|
 |
[2.39, 5.32] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 245649 | 0.01% | 956 |
| chr1 | 29341 | 0.01% | 121 |
| chr2 | 22688 | 0.01% | 82 |
| chr3 | 10443 | 0.01% | 44 |
| chr4 | 15828 | 0.01% | 59 |
| chr5 | 23378 | 0.01% | 84 |
| chr6 | 28323 | 0.02% | 112 |
| chr7 | 13808 | 0.01% | 56 |
| chr8 | 7494 | 0.01% | 32 |
| chr9 | 8932 | 0.01% | 36 |
| chr10 | 14328 | 0.01% | 46 |
| chr11 | 8888 | 0.01% | 32 |
| chr12 | 9007 | 0.01% | 35 |
| chr13 | 11053 | 0.01% | 40 |
| chr14 | 5636 | 0.01% | 24 |
| chr15 | 12058 | 0.01% | 47 |
| chr16 | 5668 | 0.01% | 19 |
| chr17 | 6509 | 0.01% | 30 |
| chr18 | 2700 | <0.01% | 13 |
| chr19 | 2361 | <0.01% | 11 |
| chr20 | 4136 | 0.01% | 21 |
| chr21 | 716 | <0.01% | 3 |
| chr22 | 2354 | <0.01% | 9 |
| 3344 contigs with no values (342345395 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 956 | 145 | 1321 | 256.96 | 219.5 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF394LUW.bed.gz | 15.5 KB | 5748318ed867a5638b83221985530f8a |
| ENCFF394LUW.tabix.bed.gz | 9.18 KB | e83825522ca0fa351173c03769533656 |
| ENCFF394LUW.tabix.bed.gz.tbi | 11.38 KB | 4bf5a95c82a9b3d3ff3fa453af9201bb |
| genomic_resource.yaml | 3.75 KB | 6c4888b10d6dd05783e6adef7b19c543 |
| statistics/ |