Resource
| Id | Histone_ChIP-seq/ENCSR000ASF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ASF [biosample_summary="Homo sapiens fibroblast of lung female child (11 years) and male adult (45 years)" and target="H3K79me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (45 years) female child (11 years) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN176WBT|/analyses/ENCAN176WBT/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF649JWQ|/files/ENCFF649JWQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 26488130 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_not_compliant: Processed alignments file {ENCFF882JAM|/files/ENCFF882JAM/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 24344287 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 {ENCFF882JAM|/files/ENCFF882JAM/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF882JAM|/files/ENCFF882JAM/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.17. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ASF | float |
Histone_ChIP-seq_ENCSR000ASF |
Histone_ChIP-seq ENCSR000ASF [biosample_summary="Homo sapiens fibroblast of lung female child (11 years) and male adult (45 years)" and target="H3K79me2"]
|
 |
[2.01, 32.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 68671237 | 2.13% | 117331 |
| chr1 | 6596649 | 2.65% | 11188 |
| chr2 | 5768554 | 2.38% | 9340 |
| chr3 | 4691474 | 2.37% | 8305 |
| chr4 | 3061787 | 1.61% | 5462 |
| chr5 | 3938620 | 2.17% | 6305 |
| chr6 | 3323635 | 1.95% | 5993 |
| chr7 | 3530726 | 2.22% | 6222 |
| chr8 | 3062690 | 2.11% | 4952 |
| chr9 | 2852126 | 2.06% | 4961 |
| chr10 | 3542706 | 2.65% | 6462 |
| chr11 | 3465014 | 2.57% | 5569 |
| chr12 | 3758360 | 2.82% | 6376 |
| chr13 | 1745797 | 1.53% | 3135 |
| chr14 | 2136715 | 2.00% | 3690 |
| chr15 | 2544102 | 2.49% | 4610 |
| chr16 | 2460585 | 2.72% | 4173 |
| chr17 | 3283149 | 3.94% | 5517 |
| chr18 | 1174704 | 1.46% | 2064 |
| chr19 | 2704157 | 4.61% | 4300 |
| chr20 | 1769830 | 2.75% | 2975 |
| chr21 | 722002 | 1.55% | 1118 |
| chr22 | 1414696 | 2.78% | 2433 |
| chrX | 1112129 | 0.71% | 2148 |
| chrY | 11030 | 0.02% | 33 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 117331 | 120 | 26701 | 585.28 | 322 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF958IYH.bed.gz | 2.33 MB | 58df968429bd1d4d99fa4264fe04b917 |
| ENCFF958IYH.tabix.bed.gz | 1.16 MB | a8cf2255398d896fdf99a8e959ddddb4 |
| ENCFF958IYH.tabix.bed.gz.tbi | 125.74 KB | 8cc16e8856d208c45dfbaa3d796dc751 |
| genomic_resource.yaml | 3.86 KB | 0e5e49610051d2b1fe90c66e409e488b |
| statistics/ |