Resource
| Id | Histone_ChIP-seq/ENCSR536SZD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR536SZD [biosample_summary="Homo sapiens NCI-H929" and target="H3F3A"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN700AAK|/analyses/ENCAN700AAK/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF678EEL|/files/ENCFF678EEL/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 27903305 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3F3A-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: Processed alignments file {ENCFF806GPM|/files/ENCFF806GPM/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 35871436 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3F3A-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 {ENCFF806GPM|/files/ENCFF806GPM/} 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 {ENCFF806GPM|/files/ENCFF806GPM/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.93. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR536SZD | float |
Histone_ChIP-seq_ENCSR536SZD |
Histone_ChIP-seq ENCSR536SZD [biosample_summary="Homo sapiens NCI-H929" and target="H3F3A"]
|
 |
[1.52, 9.46] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 17417222 | 0.54% | 21926 |
| chr1 | 2198312 | 0.88% | 2614 |
| chr2 | 1266133 | 0.52% | 1556 |
| chr3 | 1198388 | 0.60% | 1489 |
| chr4 | 597403 | 0.31% | 799 |
| chr5 | 1267271 | 0.70% | 1508 |
| chr6 | 1153978 | 0.68% | 1301 |
| chr7 | 639298 | 0.40% | 864 |
| chr8 | 912486 | 0.63% | 1069 |
| chr9 | 505461 | 0.37% | 731 |
| chr10 | 591543 | 0.44% | 811 |
| chr11 | 912321 | 0.68% | 1156 |
| chr12 | 773505 | 0.58% | 978 |
| chr13 | 53974 | 0.05% | 101 |
| chr14 | 600828 | 0.56% | 757 |
| chr15 | 540991 | 0.53% | 734 |
| chr16 | 685604 | 0.76% | 847 |
| chr17 | 944625 | 1.13% | 1238 |
| chr18 | 272178 | 0.34% | 383 |
| chr19 | 892745 | 1.52% | 1184 |
| chr20 | 616961 | 0.96% | 734 |
| chr21 | 155554 | 0.33% | 202 |
| chr22 | 433109 | 0.85% | 556 |
| chrX | 204554 | 0.13% | 314 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 21926 | 193 | 31429 | 794.36 | 571 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF718YSW.bed.gz | 493.64 KB | f506a726f7423f73763b850fd3b3385b |
| ENCFF718YSW.tabix.bed.gz | 232.9 KB | 3d9ef76185e896ce0f0631f5a73cc1f4 |
| ENCFF718YSW.tabix.bed.gz.tbi | 97.05 KB | 20f31340f152480d5f8135ebdd389f71 |
| genomic_resource.yaml | 3.69 KB | 95095a7b31610ebc16b07dbd98fa061d |
| statistics/ |