Resource
| Id | Histone_ChIP-seq/ENCSR466DUB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR466DUB [biosample_summary="Homo sapiens spleen tissue male adult (34 years)" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN996IFR|/analyses/ENCAN996IFR/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF011YZH|/files/ENCFF011YZH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18084377 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 alignments file {ENCFF011YZH|/files/ENCFF011YZH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF011YZH|/files/ENCFF011YZH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.11. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR466DUB | float |
Histone_ChIP-seq_ENCSR466DUB |
Histone_ChIP-seq ENCSR466DUB [biosample_summary="Homo sapiens spleen tissue male adult (34 years)" and target="H3K36me3"]
|
 |
[2, 39.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 63425482 | 1.97% | 108921 |
| chr1 | 5731203 | 2.30% | 10332 |
| chr1_KI270711v1_random | 256 | 0.61% | 1 |
| chr1_KI270712v1_random | 521 | 0.30% | 1 |
| chr2 | 3790610 | 1.57% | 7466 |
| chr3 | 3323973 | 1.68% | 6063 |
| chr4 | 1659490 | 0.87% | 3195 |
| chr5 | 2212575 | 1.22% | 4228 |
| chr6 | 2402828 | 1.41% | 4581 |
| chr7 | 2991205 | 1.88% | 5260 |
| chr8 | 1908043 | 1.31% | 3626 |
| chr9 | 3145414 | 2.27% | 5196 |
| chr10 | 2472443 | 1.85% | 4818 |
| chr11 | 3602492 | 2.67% | 5771 |
| chr12 | 3310440 | 2.48% | 5674 |
| chr13 | 898337 | 0.79% | 1931 |
| chr14 | 1967217 | 1.84% | 3654 |
| chr15 | 1972875 | 1.93% | 3733 |
| chr16 | 4175361 | 4.62% | 6285 |
| chr17 | 4568855 | 5.49% | 7087 |
| chr17_GL000205v2_random | 331 | 0.18% | 1 |
| chr18 | 741521 | 0.92% | 1585 |
| chr19 | 5341371 | 9.11% | 7173 |
| chr20 | 2424256 | 3.76% | 3938 |
| chr21 | 1000702 | 2.14% | 1643 |
| chr22 | 2875553 | 5.66% | 4122 |
| chr22_KI270736v1_random | 496 | 0.27% | 2 |
| chrUn_GL000219v1 | 923 | 0.52% | 3 |
| chrUn_KI270442v1 | 481 | 0.12% | 1 |
| chrX | 884297 | 0.57% | 1508 |
| chrY | 21413 | 0.04% | 43 |
| 3336 contigs with no values (127920062 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 108921 | 145 | 12267 | 582.31 | 400 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF224MXB.bed.gz | 2.17 MB | 0e196cafa770c749b196d7a2616949b9 |
| ENCFF224MXB.tabix.bed.gz | 1.04 MB | c9e1f07c596af15245ecb1411fd845f1 |
| ENCFF224MXB.tabix.bed.gz.tbi | 189.19 KB | 6a85250625ce814bbe9808675ec7b0d6 |
| genomic_resource.yaml | 3.22 KB | deb8e74bfae6c6e346c9b4f012e6158b |
| statistics/ |