Resource
| Id | DNase-seq/ENCSR000ELR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000ELR [biosample_summary="Homo sapiens hepatic stellate cell female adult (59 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (59 years) output_type: peaks audit_error: Alignment file {ENCFF938QTJ|/files/ENCFF938QTJ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 368818 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/}) audit_internal_action: Archived analysis {ENCAN808SYS|/analyses/ENCAN808SYS/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} 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 {ENCFF938QTJ|/files/ENCFF938QTJ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.26. 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000ELR | float |
DNase-seq_ENCSR000ELR |
DNase-seq ENCSR000ELR [biosample_summary="Homo sapiens hepatic stellate cell female adult (59 years)"]
|
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[6, 48] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 23400 | <0.01% | 156 |
| chr1 | 1950 | <0.01% | 13 |
| chr2 | 1050 | <0.01% | 7 |
| chr3 | 1800 | <0.01% | 12 |
| chr4 | 1050 | <0.01% | 7 |
| chr5 | 1350 | <0.01% | 9 |
| chr6 | 600 | <0.01% | 4 |
| chr7 | 1350 | <0.01% | 9 |
| chr8 | 1200 | <0.01% | 8 |
| chr9 | 1350 | <0.01% | 9 |
| chr10 | 450 | <0.01% | 3 |
| chr11 | 750 | <0.01% | 5 |
| chr12 | 1650 | <0.01% | 11 |
| chr13 | 300 | <0.01% | 2 |
| chr14 | 300 | <0.01% | 2 |
| chr15 | 1200 | <0.01% | 8 |
| chr16 | 900 | <0.01% | 6 |
| chr17 | 1500 | <0.01% | 10 |
| chr18 | 150 | <0.01% | 1 |
| chr19 | 2700 | <0.01% | 18 |
| chr20 | 1200 | <0.01% | 8 |
| chr21 | 150 | <0.01% | 1 |
| chr22 | 450 | <0.01% | 3 |
| 3344 contigs with no values (342345395 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 156 | 150 | 150 | 150 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF801KLJ.bed.gz | 1.8 KB | b87f0ac776f01076e505d6b6c15c2c46 |
| ENCFF801KLJ.tabix.bed.gz | 1.49 KB | b2a78583dce4a388a18ed149cf81d8bf |
| ENCFF801KLJ.tabix.bed.gz.tbi | 5.26 KB | a6a029023d47f0f0262a6022356d3c22 |
| genomic_resource.yaml | 2.81 KB | f9d1c6ca6c1ebbc63240958ed209105e |
| statistics/ |
