Resource
| Id | Histone_ChIP-seq/ENCSR000DWZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DWZ [biosample_summary="Homo sapiens fibroblast of lung male adult (45 years)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (45 years) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN982FHJ|/analyses/ENCAN982FHJ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF235IZE|/files/ENCFF235IZE/} processed by ChIP-seq ENCODE3 hg19 pipeline has 15204472 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: Processed alignments file {ENCFF770TPW|/files/ENCFF770TPW/} processed by ChIP-seq ENCODE3 hg19 pipeline has 19211021 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 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 {ENCFF235IZE|/files/ENCFF235IZE/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF235IZE|/files/ENCFF235IZE/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.06. 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 {ENCFF770TPW|/files/ENCFF770TPW/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF770TPW|/files/ENCFF770TPW/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.83. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DWZ | float |
Histone_ChIP-seq_ENCSR000DWZ |
Histone_ChIP-seq ENCSR000DWZ [biosample_summary="Homo sapiens fibroblast of lung male adult (45 years)" and target="H3K4me3"]
|
 |
[1.73, 138] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 48635518 | 1.51% | 34488 |
| chr1 | 4745711 | 1.91% | 3324 |
| chr2 | 3349991 | 1.38% | 2438 |
| chr3 | 2830702 | 1.43% | 1930 |
| chr4 | 2057657 | 1.08% | 1444 |
| chr5 | 2416673 | 1.33% | 1670 |
| chr6 | 2899653 | 1.70% | 1988 |
| chr7 | 2322333 | 1.46% | 1680 |
| chr8 | 1880023 | 1.30% | 1337 |
| chr9 | 2034026 | 1.47% | 1514 |
| chr10 | 2063345 | 1.54% | 1493 |
| chr11 | 2657729 | 1.97% | 1794 |
| chr12 | 2676327 | 2.01% | 1762 |
| chr13 | 1020268 | 0.89% | 785 |
| chr14 | 1568658 | 1.47% | 1082 |
| chr15 | 1612469 | 1.58% | 1135 |
| chr16 | 1835414 | 2.03% | 1355 |
| chr17 | 2753853 | 3.31% | 1955 |
| chr18 | 840400 | 1.05% | 673 |
| chr19 | 2815443 | 4.80% | 2057 |
| chr20 | 1211402 | 1.88% | 875 |
| chr21 | 492191 | 1.05% | 384 |
| chr22 | 1025235 | 2.02% | 762 |
| chrX | 1471671 | 0.94% | 1024 |
| chrY | 54344 | 0.09% | 27 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 34488 | 185 | 32767 | 1410.22 | 873 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF865HDE.bed.gz | 905.2 KB | 04595fb622fd7915300dfb640c7b702d |
| ENCFF865HDE.tabix.bed.gz | 389.25 KB | 2ab65da70e32accf4d1d879010a57a7f |
| ENCFF865HDE.tabix.bed.gz.tbi | 185.76 KB | 49f84770366cae716f33ed44eb0aa4f1 |
| genomic_resource.yaml | 4.95 KB | 6640c9e9243c1ba97cb444f15f3f6a59 |
| statistics/ |