Resource
| Id | DNase-seq/ENCSR000EPF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EPF [biosample_summary="Homo sapiens LNCaP clone FGC"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: peaks audit_warning: Alignment file {ENCFF082JPF|/files/ENCFF082JPF/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 27792392 mapped reads. According to ENCODE standards, conventional DNase-seq profile requires a minimum of 20 million uniquely mapped reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) audit_warning: Alignment file {ENCFF906VSV|/files/ENCFF906VSV/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 36175293 mapped reads. According to ENCODE standards, conventional DNase-seq profile requires a minimum of 20 million uniquely mapped reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000EPF | float |
DNase-seq_ENCSR000EPF |
DNase-seq ENCSR000EPF [biosample_summary="Homo sapiens LNCaP clone FGC"]
|
 |
[0.218, 46] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 16965321 | 0.53% | 97337 |
| chr1 | 1522649 | 0.61% | 8725 |
| chr2 | 1203432 | 0.50% | 6993 |
| chr3 | 1238846 | 0.62% | 7113 |
| chr4 | 993976 | 0.52% | 5710 |
| chr5 | 1024755 | 0.56% | 5887 |
| chr6 | 1050091 | 0.61% | 6013 |
| chr7 | 900561 | 0.57% | 5175 |
| chr8 | 828355 | 0.57% | 4758 |
| chr9 | 694635 | 0.50% | 4022 |
| chr10 | 822162 | 0.61% | 4761 |
| chr11 | 841145 | 0.62% | 4838 |
| chr12 | 845153 | 0.63% | 4853 |
| chr13 | 426350 | 0.37% | 2475 |
| chr14 | 586636 | 0.55% | 3359 |
| chr15 | 562646 | 0.55% | 3192 |
| chr16 | 496343 | 0.55% | 2854 |
| chr17 | 635090 | 0.76% | 3604 |
| chr18 | 414078 | 0.52% | 2375 |
| chr19 | 491202 | 0.84% | 2635 |
| chr20 | 400609 | 0.62% | 2307 |
| chr21 | 220515 | 0.47% | 1252 |
| chr22 | 252756 | 0.50% | 1455 |
| chrX | 477753 | 0.31% | 2761 |
| chrY | 35583 | 0.06% | 220 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 97337 | 7 | 700 | 174.29 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF422MXW.bed.gz | 1.01 MB | d987cdab7f470e4fe1e020d9801af944 |
| ENCFF422MXW.tabix.bed.gz | 925.83 KB | 29d84d969d07637039ea7f6a2b2decb5 |
| ENCFF422MXW.tabix.bed.gz.tbi | 489.24 KB | 18c6eca6650c3304f1b9c7a265c6e983 |
| genomic_resource.yaml | 2.37 KB | ecb57235873dadf3d60a2608347c3324 |
| statistics/ |