Resource
| Id | Histone_ChIP-seq/ENCSR000APO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000APO [biosample_summary="Homo sapiens fibroblast of dermis" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN899AFH|/analyses/ENCAN899AFH/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF678BZW|/files/ENCFF678BZW/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 6859804 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-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 {ENCFF275IVB|/files/ENCFF275IVB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 25537974 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-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 {ENCFF275IVB|/files/ENCFF275IVB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF275IVB|/files/ENCFF275IVB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 5.76. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000APO | float |
Histone_ChIP-seq_ENCSR000APO |
Histone_ChIP-seq ENCSR000APO [biosample_summary="Homo sapiens fibroblast of dermis" and target="H3K27me3"]
|
 |
[1.93, 14.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12675430 | 0.39% | 41294 |
| chr1 | 1358885 | 0.55% | 4428 |
| chr1_KI270713v1_random | 647 | 1.59% | 3 |
| chr2 | 1010715 | 0.42% | 3316 |
| chr3 | 702390 | 0.35% | 2417 |
| chr4 | 465930 | 0.24% | 1541 |
| chr5 | 701945 | 0.39% | 2327 |
| chr6 | 722299 | 0.42% | 2291 |
| chr7 | 574118 | 0.36% | 1802 |
| chr8 | 573602 | 0.40% | 1945 |
| chr9 | 605499 | 0.44% | 1910 |
| chr10 | 752504 | 0.56% | 2463 |
| chr11 | 718460 | 0.53% | 2386 |
| chr12 | 585775 | 0.44% | 1840 |
| chr13 | 366723 | 0.32% | 1122 |
| chr14 | 402612 | 0.38% | 1233 |
| chr15 | 548386 | 0.54% | 1805 |
| chr16 | 302900 | 0.34% | 997 |
| chr17 | 748136 | 0.90% | 2178 |
| chr18 | 254080 | 0.32% | 861 |
| chr19 | 315354 | 0.54% | 960 |
| chr20 | 414184 | 0.64% | 1424 |
| chr21 | 163020 | 0.35% | 538 |
| chr22 | 217362 | 0.43% | 769 |
| chrX | 169904 | 0.11% | 738 |
| 3342 contigs with no values (186263755 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41294 | 135 | 6044 | 306.96 | 225 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF450JBC.bed.gz | 718.85 KB | 0436099a503a50c369209b933f769a61 |
| ENCFF450JBC.tabix.bed.gz | 387.91 KB | 69c7709f3fe4d30efcdd7006fcc5b475 |
| ENCFF450JBC.tabix.bed.gz.tbi | 127.44 KB | aa8cf02686596d6c6e91dae272b3aaba |
| genomic_resource.yaml | 3.81 KB | 17859f5785f22b65ab9363a954a0df60 |
| statistics/ |