Resource
| Id | Histone_ChIP-seq/ENCSR000ARW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ARW [biosample_summary="Homo sapiens fibroblast of dermis" and target="H3K79me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_error: Processed alignments file {ENCFF581THL|/files/ENCFF581THL/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 4392949 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K79me2-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_internal_action: Released analysis {ENCAN894ZIT|/analyses/ENCAN894ZIT/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN894ZIT|/analyses/ENCAN894ZIT/} has in progress subobject document {ab096a01-8946-4992-8493-f574968155df|/documents/ab096a01-8946-4992-8493-f574968155df/} audit_not_compliant: Processed alignments file {ENCFF129EQX|/files/ENCFF129EQX/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 30349106 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K79me2-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 {ENCFF129EQX|/files/ENCFF129EQX/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.80. 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 {ENCFF129EQX|/files/ENCFF129EQX/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.22. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ARW | float |
Histone_ChIP-seq_ENCSR000ARW |
Histone_ChIP-seq ENCSR000ARW [biosample_summary="Homo sapiens fibroblast of dermis" and target="H3K79me2"]
|
 |
[1.66, 31.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 138791813 | 4.31% | 59848 |
| chr1 | 13401938 | 5.38% | 5818 |
| chr2 | 10913569 | 4.51% | 4463 |
| chr3 | 9626434 | 4.85% | 3985 |
| chr4 | 6395414 | 3.36% | 2872 |
| chr5 | 7539321 | 4.15% | 3108 |
| chr6 | 7047019 | 4.13% | 3219 |
| chr7 | 7367104 | 4.62% | 3315 |
| chr8 | 5850434 | 4.03% | 2374 |
| chr9 | 5778969 | 4.18% | 2509 |
| chr10 | 7538622 | 5.63% | 3225 |
| chr11 | 6790840 | 5.03% | 2946 |
| chr12 | 7334469 | 5.50% | 2914 |
| chr13 | 3545531 | 3.10% | 1485 |
| chr14 | 4346285 | 4.06% | 1866 |
| chr15 | 5618336 | 5.51% | 2363 |
| chr16 | 5028095 | 5.57% | 2287 |
| chr17 | 6570691 | 7.89% | 2867 |
| chr18 | 2856689 | 3.55% | 1270 |
| chr19 | 5027753 | 8.58% | 2344 |
| chr20 | 3449292 | 5.35% | 1449 |
| chr21 | 1372135 | 2.94% | 531 |
| chr22 | 3013300 | 5.93% | 1390 |
| chrX | 2379573 | 1.52% | 1248 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 59848 | 255 | 126948 | 2319.07 | 1086 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF624VMS.bed.gz | 1.45 MB | a75253aa5915fee43e1419aa3855aaf1 |
| ENCFF624VMS.tabix.bed.gz | 655.17 KB | 335515fcb6e2b47cb162d54f727599d0 |
| ENCFF624VMS.tabix.bed.gz.tbi | 112.55 KB | a8fa92dbb590e3347f324105c5dd5492 |
| genomic_resource.yaml | 4.05 KB | 3e4989353cb62f35fa5ae0b5a7a34700 |
| statistics/ |