Resource
| Id | Histone_ChIP-seq/ENCSR445RFF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR445RFF [biosample_summary="Homo sapiens sigmoid colon 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: Released analysis {ENCAN953YRK|/analyses/ENCAN953YRK/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN953YRK|/analyses/ENCAN953YRK/} has in progress subobject document {ddbd7400-97c3-47a1-b078-ec5efe87a366|/documents/ddbd7400-97c3-47a1-b078-ec5efe87a366/} audit_not_compliant: Processed alignments file {ENCFF764EJI|/files/ENCFF764EJI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 19007370 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 {ENCFF764EJI|/files/ENCFF764EJI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF764EJI|/files/ENCFF764EJI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.22. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR445RFF | float |
Histone_ChIP-seq_ENCSR445RFF |
Histone_ChIP-seq ENCSR445RFF [biosample_summary="Homo sapiens sigmoid colon tissue male adult (34 years)" and target="H3K36me3"]
|
 |
[1.81, 36.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 40660262 | 1.26% | 101275 |
| chr1 | 3934966 | 1.58% | 9989 |
| chr2 | 2504712 | 1.03% | 6974 |
| chr3 | 2175986 | 1.10% | 5818 |
| chr4 | 1268976 | 0.67% | 3523 |
| chr5 | 1595252 | 0.88% | 4363 |
| chr6 | 1582782 | 0.93% | 4275 |
| chr7 | 1887568 | 1.18% | 4788 |
| chr8 | 1211961 | 0.84% | 3343 |
| chr9 | 1929865 | 1.39% | 4605 |
| chr10 | 1578487 | 1.18% | 4394 |
| chr11 | 2301968 | 1.70% | 5391 |
| chr12 | 2254316 | 1.69% | 5528 |
| chr13 | 560277 | 0.49% | 1703 |
| chr14 | 1309580 | 1.22% | 3485 |
| chr15 | 1350677 | 1.32% | 3656 |
| chr16 | 2476300 | 2.74% | 5486 |
| chr17 | 2828002 | 3.40% | 6479 |
| chr18 | 504098 | 0.63% | 1496 |
| chr19 | 3393099 | 5.79% | 6781 |
| chr20 | 1466779 | 2.28% | 3451 |
| chr21 | 582674 | 1.25% | 1399 |
| chr22 | 1528635 | 3.01% | 3165 |
| chrX | 418441 | 0.27% | 1136 |
| chrY | 14861 | 0.03% | 47 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 101275 | 140 | 7610 | 401.48 | 303 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF406TXJ.bed.gz | 1.94 MB | 3e76fc0358defb36c562ed6a83369f32 |
| ENCFF406TXJ.tabix.bed.gz | 972.44 KB | 442217da79c21ef319dd17d039c91672 |
| ENCFF406TXJ.tabix.bed.gz.tbi | 174.07 KB | 81782310d5cc896bd9c2d5a92909e31a |
| genomic_resource.yaml | 3.48 KB | 01b9cf19e4ba1913ced9c51a149805a1 |
| statistics/ |