Resource
| Id | Histone_ChIP-seq/ENCSR080JPX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR080JPX [biosample_summary="Homo sapiens spleen tissue male adult (54 years)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (54 years) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN775WFD|/analyses/ENCAN775WFD/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF670VZJ|/files/ENCFF670VZJ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 42403232 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 {ENCFF261YAA|/files/ENCFF261YAA/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF261YAA|/files/ENCFF261YAA/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.25. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR080JPX | float |
Histone_ChIP-seq_ENCSR080JPX |
Histone_ChIP-seq ENCSR080JPX [biosample_summary="Homo sapiens spleen tissue male adult (54 years)" and target="H3K27me3"]
|
 |
[1.12, 21.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 113932777 | 3.54% | 89289 |
| chr1 | 12714519 | 5.11% | 10020 |
| chr2 | 7993853 | 3.30% | 6655 |
| chr3 | 4312952 | 2.18% | 3694 |
| chr4 | 3824314 | 2.01% | 2822 |
| chr5 | 5608479 | 3.09% | 4292 |
| chr6 | 5920822 | 3.47% | 4441 |
| chr7 | 4984259 | 3.13% | 3798 |
| chr8 | 4719709 | 3.25% | 3831 |
| chr9 | 5010437 | 3.62% | 3807 |
| chr10 | 6084692 | 4.55% | 4993 |
| chr11 | 6338353 | 4.69% | 5337 |
| chr12 | 5593011 | 4.20% | 4413 |
| chr13 | 2509569 | 2.19% | 2123 |
| chr14 | 3357142 | 3.14% | 2705 |
| chr15 | 4372709 | 4.29% | 3775 |
| chr16 | 4367072 | 4.83% | 3498 |
| chr17 | 7080829 | 8.50% | 4938 |
| chr18 | 2020459 | 2.51% | 1819 |
| chr19 | 6409506 | 10.93% | 4191 |
| chr20 | 4910235 | 7.62% | 3720 |
| chr21 | 1402464 | 3.00% | 1138 |
| chr22 | 3572005 | 7.03% | 2789 |
| chrX | 807518 | 0.52% | 473 |
| chrY | 17869 | 0.03% | 17 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 89289 | 245 | 134526 | 1276 | 690 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF141VUN.bed.gz | 1.92 MB | b1c0001d7004a1978a105e2404b46071 |
| ENCFF141VUN.tabix.bed.gz | 940.76 KB | c9c01ef7a2cfda52cfc225a0a61bff2e |
| ENCFF141VUN.tabix.bed.gz.tbi | 207.15 KB | 72c5457e4f07cf0f7b9d2b124ca83d05 |
| genomic_resource.yaml | 3.21 KB | eec10d99038a274178358fad9db1bead |
| statistics/ |