Resource
| Id | Histone_ChIP-seq/ENCSR397HSO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR397HSO [biosample_summary="Homo sapiens neural cell originated from H1" and target="H3K9me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male embryo output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN981YIR|/analyses/ENCAN981YIR/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF331MAR|/files/ENCFF331MAR/} processed by ChIP-seq ENCODE3 hg19 pipeline has 23361361 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me2-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 {ENCFF478GTE|/files/ENCFF478GTE/} 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 {ENCFF478GTE|/files/ENCFF478GTE/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.71. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR397HSO | float |
Histone_ChIP-seq_ENCSR397HSO |
Histone_ChIP-seq ENCSR397HSO [biosample_summary="Homo sapiens neural cell originated from H1" and target="H3K9me2"]
|
 |
[1.75, 3.98] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 155997 | <0.01% | 474 |
| chr1 | 15174 | 0.01% | 44 |
| chr2 | 11260 | <0.01% | 37 |
| chr3 | 11775 | 0.01% | 36 |
| chr4 | 15553 | 0.01% | 51 |
| chr5 | 12411 | 0.01% | 40 |
| chr6 | 18149 | 0.01% | 47 |
| chr7 | 7650 | <0.01% | 23 |
| chr8 | 7692 | 0.01% | 24 |
| chr9 | 4452 | <0.01% | 15 |
| chr10 | 4675 | <0.01% | 13 |
| chr11 | 4887 | <0.01% | 16 |
| chr12 | 9201 | 0.01% | 28 |
| chr13 | 8071 | 0.01% | 25 |
| chr14 | 7372 | 0.01% | 22 |
| chr15 | 3053 | <0.01% | 9 |
| chr16 | 1449 | <0.01% | 4 |
| chr17 | 1824 | <0.01% | 5 |
| chr18 | 6261 | 0.01% | 18 |
| chr20 | 1791 | <0.01% | 6 |
| chr21 | 2319 | <0.01% | 8 |
| chr22 | 978 | <0.01% | 3 |
| 3345 contigs with no values (400963011 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 474 | 194 | 1567 | 329.11 | 310 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF866CDK.bed.gz | 11.44 KB | 7916b64b920aed425708bf700a0e9e11 |
| ENCFF866CDK.tabix.bed.gz | 5.38 KB | d97c34f792fc27f725d43d19bf809c9a |
| ENCFF866CDK.tabix.bed.gz.tbi | 9.07 KB | 9c47c4e71ab6d30c6a05451bdb7ac57b |
| genomic_resource.yaml | 3.32 KB | bf0541008c43d718948bd8cbdae34f07 |
| statistics/ |