Resource
| Id | Histone_ChIP-seq/ENCSR743JIT |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR743JIT [biosample_summary="Homo sapiens iPS-18a" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN610DGF|/analyses/ENCAN610DGF/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN610DGF|/analyses/ENCAN610DGF/} has in progress subobject document {bf5584ea-b3ba-4f03-b0ad-1558742ea2b2|/documents/bf5584ea-b3ba-4f03-b0ad-1558742ea2b2/} audit_not_compliant: Processed alignments file {ENCFF189FVI|/files/ENCFF189FVI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 27088738 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 {ENCFF189FVI|/files/ENCFF189FVI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.80. 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 {ENCFF189FVI|/files/ENCFF189FVI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 4.87. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR743JIT | float |
Histone_ChIP-seq_ENCSR743JIT |
Histone_ChIP-seq ENCSR743JIT [biosample_summary="Homo sapiens iPS-18a" and target="H3K27me3"]
|
 |
[1.81, 82.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 52446247 | 1.63% | 28782 |
| chr1 | 4912987 | 1.97% | 2774 |
| chr2 | 3903884 | 1.61% | 2121 |
| chr3 | 2451971 | 1.24% | 1464 |
| chr4 | 2445196 | 1.29% | 1162 |
| chr5 | 2741643 | 1.51% | 1399 |
| chr6 | 2946383 | 1.72% | 1472 |
| chr7 | 2562272 | 1.61% | 1291 |
| chr8 | 2231745 | 1.54% | 1224 |
| chr9 | 2544746 | 1.84% | 1605 |
| chr10 | 2757133 | 2.06% | 1362 |
| chr11 | 3002857 | 2.22% | 1747 |
| chr12 | 2795035 | 2.10% | 1430 |
| chr13 | 1249662 | 1.09% | 635 |
| chr14 | 1638833 | 1.53% | 859 |
| chr15 | 1755639 | 1.72% | 932 |
| chr16 | 1561203 | 1.73% | 912 |
| chr17 | 2806597 | 3.37% | 1521 |
| chr18 | 1054613 | 1.31% | 567 |
| chr19 | 2061210 | 3.52% | 1366 |
| chr20 | 1679556 | 2.61% | 1056 |
| chr21 | 500432 | 1.07% | 288 |
| chr22 | 1577378 | 3.10% | 869 |
| chrX | 1265272 | 0.81% | 726 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 28782 | 260 | 144666 | 1822.19 | 1051 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF064BOC.bed.gz | 701.74 KB | ff51866c7a14a6e4a154dc24798484c8 |
| ENCFF064BOC.tabix.bed.gz | 317.39 KB | 479eae80741dfcce878eace930751d0c |
| ENCFF064BOC.tabix.bed.gz.tbi | 120.87 KB | ca8ef16abbf14664487668b9658866ff |
| genomic_resource.yaml | 3.42 KB | 8a883d2aadf59a068ed5bd1a6f093af5 |
| statistics/ |