Resource
| Id | DNase-seq/ENCSR000ELH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000ELH [biosample_summary="Homo sapiens keratinocyte female"] |
| Description |
status: released biological_replicates: Rep 1 summary: female output_type: peaks audit_internal_action: Released analysis {ENCAN529UAX|/analyses/ENCAN529UAX/} has in progress subobject document {39983f73-4e70-46f2-88e4-e9fd0660fc73|/documents/39983f73-4e70-46f2-88e4-e9fd0660fc73/} audit_warning: Alignment file {ENCFF117RNM|/files/ENCFF117RNM/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 35765456 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: Signal Portion of Tags (SPOT) is a measure of enrichment, analogous to the commonly used fraction of reads in peaks metric. ENCODE processed alignment files {ENCFF117RNM|/files/ENCFF117RNM/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.27. According to ENCODE standards, SPOT1 score of 0.4 or higher is considered a product of high quality data. Any sample with a SPOT1 score <0.3 should be targeted for replacement with a higher quality sample, and a SPOT1 score of 0.25 is considered minimally acceptable SPOT1 score of 0.25 is considered minimally acceptable for rare and hard to find primary tissues. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000ELH | float |
DNase-seq_ENCSR000ELH |
DNase-seq ENCSR000ELH [biosample_summary="Homo sapiens keratinocyte female"]
|
 |
[0.112, 8.17] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8143522 | 0.25% | 48915 |
| chr1 | 808579 | 0.32% | 4864 |
| chr2 | 650015 | 0.27% | 3966 |
| chr3 | 498082 | 0.25% | 2996 |
| chr4 | 362386 | 0.19% | 2234 |
| chr5 | 407750 | 0.22% | 2497 |
| chr6 | 458759 | 0.27% | 2745 |
| chr7 | 398110 | 0.25% | 2392 |
| chr8 | 350485 | 0.24% | 2146 |
| chr9 | 360872 | 0.26% | 2162 |
| chr10 | 398072 | 0.30% | 2394 |
| chr11 | 427057 | 0.32% | 2544 |
| chr12 | 418254 | 0.31% | 2516 |
| chr13 | 183785 | 0.16% | 1133 |
| chr14 | 263341 | 0.25% | 1571 |
| chr15 | 278774 | 0.27% | 1690 |
| chr16 | 306650 | 0.34% | 1782 |
| chr17 | 379966 | 0.46% | 2233 |
| chr18 | 170756 | 0.21% | 1055 |
| chr19 | 364014 | 0.62% | 2032 |
| chr20 | 235609 | 0.37% | 1411 |
| chr21 | 91015 | 0.19% | 556 |
| chr22 | 178351 | 0.35% | 1033 |
| chrX | 152840 | 0.10% | 963 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 48915 | 1 | 636 | 166.48 | 160 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF245IFS.bed.gz | 508.19 KB | f9958ec46b7d0aa248059f5499deac8f |
| ENCFF245IFS.tabix.bed.gz | 449.83 KB | 1a192d80202a93c1748431478a7d14be |
| ENCFF245IFS.tabix.bed.gz.tbi | 286.68 KB | 74ff4c587304ea812f59f00edd1efb3e |
| genomic_resource.yaml | 2.76 KB | 7ba57b79eaa821fcae0592fac6e238c5 |
| statistics/ |