Resource
| Id | Histone_ChIP-seq/ENCSR111OHT |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR111OHT [biosample_summary="Homo sapiens liver tissue male adult (31 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (31 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN880YSQ|/analyses/ENCAN880YSQ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF670OBN|/files/ENCFF670OBN/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline has 34093498 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 redacted alignments file {ENCFF670OBN|/files/ENCFF670OBN/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 redacted alignments file {ENCFF670OBN|/files/ENCFF670OBN/} processed by ChIP-seq ENCODE4 v1.7.0 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_ENCSR111OHT | float |
Histone_ChIP-seq_ENCSR111OHT |
Histone_ChIP-seq ENCSR111OHT [biosample_summary="Homo sapiens liver tissue male adult (31 years)" and target="H3K4me1"]
|
 |
[1.84, 18.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 57166542 | 1.78% | 100275 |
| chr1 | 5693321 | 2.29% | 9817 |
| chr2 | 4349421 | 1.80% | 7625 |
| chr3 | 3908614 | 1.97% | 6771 |
| chr4 | 2396783 | 1.26% | 4463 |
| chr5 | 2958944 | 1.63% | 5176 |
| chr6 | 3093612 | 1.81% | 5620 |
| chr7 | 2605239 | 1.63% | 4774 |
| chr8 | 2377762 | 1.64% | 4347 |
| chr9 | 2794855 | 2.02% | 4685 |
| chr10 | 2823236 | 2.11% | 4949 |
| chr11 | 3176928 | 2.35% | 5403 |
| chr12 | 2984699 | 2.24% | 5228 |
| chr13 | 1246400 | 1.09% | 2388 |
| chr14 | 1862048 | 1.74% | 3206 |
| chr15 | 1988340 | 1.95% | 3496 |
| chr16 | 2240102 | 2.48% | 3774 |
| chr17 | 2856732 | 3.43% | 4762 |
| chr18 | 1102433 | 1.37% | 2035 |
| chr19 | 2056856 | 3.51% | 3519 |
| chr20 | 1607443 | 2.49% | 2786 |
| chr21 | 540802 | 1.16% | 954 |
| chr22 | 1478296 | 2.91% | 2338 |
| chrX | 1023676 | 0.66% | 2159 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 100275 | 165 | 8170 | 570.1 | 437 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF953NPP.bed.gz | 1.94 MB | e16b46f3ea3219ce473d347de79df836 |
| ENCFF953NPP.tabix.bed.gz | 1014.14 KB | 813e89f2899822dfd4c4dc2701bca96e |
| ENCFF953NPP.tabix.bed.gz.tbi | 279.82 KB | 4734d8e08a78e554f9db930536d40733 |
| genomic_resource.yaml | 3.26 KB | 5a28be000787ee5ea2561857a850d012 |
| statistics/ |