Resource
| Id | Histone_ChIP-seq/ENCSR352UID |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR352UID [biosample_summary="Homo sapiens iPS-20b" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN342SVS|/analyses/ENCAN342SVS/} has in progress subobject document {23b554ea-94fd-49b0-ade9-9a48d6d48045|/documents/23b554ea-94fd-49b0-ade9-9a48d6d48045/} audit_internal_action: Released analysis {ENCAN342SVS|/analyses/ENCAN342SVS/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF790XUK|/files/ENCFF790XUK/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 23253539 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 {ENCFF255ECT|/files/ENCFF255ECT/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 21842361 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 {ENCFF790XUK|/files/ENCFF790XUK/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF790XUK|/files/ENCFF790XUK/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.54. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR352UID | float |
Histone_ChIP-seq_ENCSR352UID |
Histone_ChIP-seq ENCSR352UID [biosample_summary="Homo sapiens iPS-20b" and target="H3K27me3"]
|
 |
[1.64, 97.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 70021395 | 2.18% | 39630 |
| chr1 | 6974207 | 2.80% | 4121 |
| chr2 | 5246350 | 2.17% | 2870 |
| chr3 | 3304973 | 1.67% | 1981 |
| chr4 | 2956227 | 1.55% | 1480 |
| chr5 | 3515912 | 1.94% | 1870 |
| chr6 | 3834180 | 2.24% | 2044 |
| chr7 | 3261239 | 2.05% | 1704 |
| chr8 | 2895401 | 1.99% | 1629 |
| chr9 | 3068679 | 2.22% | 1800 |
| chr10 | 3505665 | 2.62% | 1866 |
| chr11 | 4292873 | 3.18% | 2538 |
| chr12 | 3779973 | 2.84% | 2077 |
| chr13 | 1516997 | 1.33% | 783 |
| chr14 | 2167688 | 2.03% | 1170 |
| chr15 | 2354503 | 2.31% | 1377 |
| chr16 | 2263793 | 2.51% | 1401 |
| chr17 | 3847722 | 4.62% | 2183 |
| chr18 | 1406033 | 1.75% | 748 |
| chr19 | 2821303 | 4.81% | 1852 |
| chr20 | 2687664 | 4.17% | 1731 |
| chr21 | 600116 | 1.28% | 341 |
| chr22 | 2205049 | 4.34% | 1226 |
| chrX | 1444490 | 0.93% | 801 |
| chrY | 70358 | 0.12% | 37 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 39630 | 228 | 150273 | 1766.88 | 981 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF248UOT.bed.gz | 963.02 KB | d9fe42929cb171aca71fa15b46bee7ef |
| ENCFF248UOT.tabix.bed.gz | 433.49 KB | addac0139d22418e99fc43a10830d528 |
| ENCFF248UOT.tabix.bed.gz.tbi | 139.42 KB | 28cf8cf98188a939779d0feb81449d25 |
| genomic_resource.yaml | 3.93 KB | 9e1a549be6ad3122c13448b20a1fbd22 |
| statistics/ |