Resource
| Id | Histone_ChIP-seq/ENCSR585KLQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR585KLQ [biosample_summary="Homo sapiens liver tissue male adult (78 years)" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (78 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN611YJV|/analyses/ENCAN611YJV/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF349CAM|/files/ENCFF349CAM/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline has 14743225 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-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 redacted alignments file {ENCFF349CAM|/files/ENCFF349CAM/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 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 redacted alignments file {ENCFF349CAM|/files/ENCFF349CAM/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 7.53. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR585KLQ | float |
Histone_ChIP-seq_ENCSR585KLQ |
Histone_ChIP-seq ENCSR585KLQ [biosample_summary="Homo sapiens liver tissue male adult (78 years)" and target="H3K36me3"]
|
 |
[2.01, 19] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 56202632 | 1.75% | 104777 |
| chr1 | 5817503 | 2.34% | 10578 |
| chr2 | 4472755 | 1.85% | 8494 |
| chr3 | 3737202 | 1.88% | 6959 |
| chr4 | 2304824 | 1.21% | 4593 |
| chr5 | 2956794 | 1.63% | 5636 |
| chr6 | 2689959 | 1.57% | 5090 |
| chr7 | 2508146 | 1.57% | 4941 |
| chr8 | 1886802 | 1.30% | 3668 |
| chr9 | 2476879 | 1.79% | 4450 |
| chr10 | 2600959 | 1.94% | 4879 |
| chr11 | 2936457 | 2.17% | 5126 |
| chr12 | 3349892 | 2.51% | 6026 |
| chr13 | 1215451 | 1.06% | 2402 |
| chr14 | 2010353 | 1.88% | 3707 |
| chr15 | 2059186 | 2.02% | 3937 |
| chr16 | 2260648 | 2.50% | 4105 |
| chr17 | 2824656 | 3.39% | 5109 |
| chr18 | 885979 | 1.10% | 1764 |
| chr19 | 3042697 | 5.19% | 4969 |
| chr20 | 1527120 | 2.37% | 2627 |
| chr21 | 592757 | 1.27% | 1120 |
| chr22 | 1190844 | 2.34% | 2088 |
| chrX | 812925 | 0.52% | 2375 |
| chrY | 41844 | 0.07% | 134 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 104777 | 155 | 8970 | 536.4 | 412 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF050ODT.bed.gz | 1.92 MB | b0821f4fa82bc4eceb16c0362bca825e |
| ENCFF050ODT.tabix.bed.gz | 995.77 KB | c206f871e3dd4f7b23dc848f57abc5e6 |
| ENCFF050ODT.tabix.bed.gz.tbi | 181.2 KB | 730a93bff3102ed3c7ad6a5309257cdb |
| genomic_resource.yaml | 3.27 KB | 86adb13b543e858a3487ce13f54c52b3 |
| statistics/ |