Resource
| Id | DNase-seq/ENCSR868XPR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR868XPR [biosample_summary="Homo sapiens muscle of arm tissue male embryo (115 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (115 days) output_type: peaks audit_warning: Alignment file {ENCFF176PMR|/files/ENCFF176PMR/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 29056603 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 {ENCFF176PMR|/files/ENCFF176PMR/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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_ENCSR868XPR | float |
DNase-seq_ENCSR868XPR |
DNase-seq ENCSR868XPR [biosample_summary="Homo sapiens muscle of arm tissue male embryo (115 days)"]
|
 |
[0.276, 15.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8246786 | 0.26% | 45747 |
| chr1 | 730924 | 0.29% | 4078 |
| chr2 | 679979 | 0.28% | 3782 |
| chr3 | 564270 | 0.28% | 3134 |
| chr4 | 442640 | 0.23% | 2455 |
| chr5 | 494568 | 0.27% | 2724 |
| chr6 | 517712 | 0.30% | 2824 |
| chr7 | 419511 | 0.26% | 2363 |
| chr8 | 399867 | 0.28% | 2242 |
| chr9 | 346022 | 0.25% | 1921 |
| chr10 | 386193 | 0.29% | 2176 |
| chr11 | 410929 | 0.30% | 2260 |
| chr12 | 417497 | 0.31% | 2305 |
| chr13 | 245302 | 0.21% | 1355 |
| chr14 | 267809 | 0.25% | 1478 |
| chr15 | 264425 | 0.26% | 1457 |
| chr16 | 235849 | 0.26% | 1321 |
| chr17 | 308364 | 0.37% | 1706 |
| chr18 | 184894 | 0.23% | 1067 |
| chr19 | 301440 | 0.51% | 1561 |
| chr20 | 191947 | 0.30% | 1077 |
| chr21 | 97688 | 0.21% | 531 |
| chr22 | 118958 | 0.23% | 679 |
| chrX | 212792 | 0.14% | 1211 |
| chrY | 7206 | 0.01% | 40 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 45747 | 1 | 800 | 180.27 | 177 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF157GNV.bed.gz | 481.65 KB | 53a9d0e46f731d333523572b304f191d |
| ENCFF157GNV.tabix.bed.gz | 426.82 KB | 2bfdc56a877f88f95ed0baed97255904 |
| ENCFF157GNV.tabix.bed.gz.tbi | 278.39 KB | 3a8580140b34ee7b46edd124d14bf3c8 |
| genomic_resource.yaml | 2.66 KB | 231bf5f3e5153d92d7876e6f482d7ef1 |
| statistics/ |