Resource
| Id | DNase-seq/ENCSR261RWJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR261RWJ [biosample_summary="Homo sapiens Peyer''s patch tissue female adult (51 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (51 years) output_type: peaks audit_internal_action: Archived analysis {ENCAN921VLI|/analyses/ENCAN921VLI/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF732ROP|/files/ENCFF732ROP/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL202DNS|/pipelines/ENCPL202DNS/} ) for GRCh38 assembly has 39488148 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_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 {ENCFF732ROP|/files/ENCFF732ROP/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR261RWJ | float |
DNase-seq_ENCSR261RWJ |
DNase-seq ENCSR261RWJ [biosample_summary="Homo sapiens Peyer''s patch tissue female adult (51 years)"]
|
 |
[6, 4.22e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6351713 | 0.20% | 42281 |
| chr1 | 649041 | 0.26% | 4321 |
| chr2 | 450175 | 0.19% | 2995 |
| chr3 | 362886 | 0.18% | 2409 |
| chr4 | 225776 | 0.12% | 1499 |
| chr5 | 285609 | 0.16% | 1898 |
| chr6 | 384842 | 0.23% | 2565 |
| chr7 | 291055 | 0.18% | 1938 |
| chr8 | 253888 | 0.17% | 1688 |
| chr9 | 267767 | 0.19% | 1779 |
| chr10 | 279485 | 0.21% | 1863 |
| chr11 | 325833 | 0.24% | 2170 |
| chr12 | 328679 | 0.25% | 2186 |
| chr13 | 130601 | 0.11% | 872 |
| chr14 | 215392 | 0.20% | 1438 |
| chr15 | 203220 | 0.20% | 1354 |
| chr16 | 255069 | 0.28% | 1698 |
| chr17 | 364274 | 0.44% | 2423 |
| chr18 | 99776 | 0.12% | 666 |
| chr19 | 392593 | 0.67% | 2616 |
| chr20 | 171860 | 0.27% | 1146 |
| chr21 | 69174 | 0.15% | 461 |
| chr22 | 168148 | 0.33% | 1119 |
| chrX | 176120 | 0.11% | 1174 |
| chrY | 450 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 42281 | 22 | 300 | 150.23 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF977PNH.bed.gz | 423.75 KB | 6051e15d7434c1bcfbcae347fcb71688 |
| ENCFF977PNH.tabix.bed.gz | 362.21 KB | e4749cbf4f83b64f6c971c146a4359a1 |
| ENCFF977PNH.tabix.bed.gz.tbi | 213.79 KB | f00d93255c8904b4560b7edada11318a |
| genomic_resource.yaml | 2.81 KB | b78e77cf929853e6a2a96a6864fa80b3 |
| statistics/ |