Resource
| Id | Histone_ChIP-seq/ENCSR111WGZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR111WGZ [biosample_summary="Homo sapiens heart left ventricle tissue male adult (34 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN675GER|/analyses/ENCAN675GER/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN675GER|/analyses/ENCAN675GER/} has in progress subobject document {a94b3c75-e250-4ee3-936e-9692bd27b530|/documents/a94b3c75-e250-4ee3-936e-9692bd27b530/} audit_not_compliant: Processed alignments file {ENCFF018JTV|/files/ENCFF018JTV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 26166780 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-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 {ENCFF018JTV|/files/ENCFF018JTV/} 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 {ENCFF018JTV|/files/ENCFF018JTV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.65. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR111WGZ | float |
Histone_ChIP-seq_ENCSR111WGZ |
Histone_ChIP-seq ENCSR111WGZ [biosample_summary="Homo sapiens heart left ventricle tissue male adult (34 years)" and target="H3K4me1"]
|
 |
[1.61, 20.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 51555749 | 1.60% | 149736 |
| chr1 | 5111019 | 2.05% | 14516 |
| chr2 | 4081791 | 1.69% | 12282 |
| chr3 | 3318730 | 1.67% | 10231 |
| chr4 | 1493105 | 0.78% | 5091 |
| chr5 | 2484963 | 1.37% | 7744 |
| chr6 | 2330424 | 1.36% | 7827 |
| chr7 | 2323968 | 1.46% | 7259 |
| chr8 | 2031261 | 1.40% | 6365 |
| chr9 | 2443399 | 1.77% | 6550 |
| chr10 | 3004187 | 2.25% | 8365 |
| chr11 | 2990983 | 2.21% | 8133 |
| chr12 | 2347581 | 1.76% | 6768 |
| chr13 | 1072611 | 0.94% | 3524 |
| chr14 | 1749396 | 1.63% | 4920 |
| chr15 | 1941401 | 1.90% | 5710 |
| chr16 | 2053451 | 2.27% | 5489 |
| chr17 | 3028026 | 3.64% | 7686 |
| chr18 | 984925 | 1.23% | 3206 |
| chr19 | 2199391 | 3.75% | 5191 |
| chr20 | 1597731 | 2.48% | 4521 |
| chr21 | 527575 | 1.13% | 1589 |
| chr22 | 1761992 | 3.47% | 4393 |
| chrX | 654577 | 0.42% | 2277 |
| chrY | 23262 | 0.04% | 99 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 149736 | 135 | 15037 | 344.31 | 265 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF569RXT.bed.gz | 3.09 MB | 25e198d80cf15c620eeb8a59b3de8495 |
| ENCFF569RXT.tabix.bed.gz | 1.45 MB | 91ddd764ace2cec6b37e562ab23568d4 |
| ENCFF569RXT.tabix.bed.gz.tbi | 350.83 KB | f697150bee1aedc071007686793581e0 |
| genomic_resource.yaml | 3.49 KB | ef7596e2ebaedfe9f24526216038ec03 |
| statistics/ |