Resource
| Id | DNase-seq/ENCSR698CUE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR698CUE [biosample_summary="Homo sapiens muscle of back tissue male embryo (96 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (96 days) output_type: peaks audit_warning: Alignment file {ENCFF794PDW|/files/ENCFF794PDW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 25598938 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 {ENCFF794PDW|/files/ENCFF794PDW/} 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_ENCSR698CUE | float |
DNase-seq_ENCSR698CUE |
DNase-seq ENCSR698CUE [biosample_summary="Homo sapiens muscle of back tissue male embryo (96 days)"]
|
 |
[0.196, 12.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7036088 | 0.22% | 37520 |
| chr1 | 637876 | 0.26% | 3374 |
| chr2 | 573184 | 0.24% | 3042 |
| chr3 | 447785 | 0.23% | 2410 |
| chr4 | 358990 | 0.19% | 1901 |
| chr5 | 389865 | 0.21% | 2082 |
| chr6 | 449560 | 0.26% | 2334 |
| chr7 | 340174 | 0.21% | 1848 |
| chr8 | 328069 | 0.23% | 1819 |
| chr9 | 303585 | 0.22% | 1635 |
| chr10 | 316660 | 0.24% | 1729 |
| chr11 | 375207 | 0.28% | 1981 |
| chr12 | 364660 | 0.27% | 1907 |
| chr13 | 177261 | 0.15% | 957 |
| chr14 | 230115 | 0.21% | 1215 |
| chr15 | 225900 | 0.22% | 1233 |
| chr16 | 217539 | 0.24% | 1156 |
| chr17 | 284880 | 0.34% | 1531 |
| chr18 | 148439 | 0.18% | 815 |
| chr19 | 325859 | 0.56% | 1606 |
| chr20 | 178551 | 0.28% | 959 |
| chr21 | 79369 | 0.17% | 427 |
| chr22 | 121146 | 0.24% | 657 |
| chrX | 155059 | 0.10% | 873 |
| chrY | 6355 | 0.01% | 29 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 37520 | 2 | 840 | 187.53 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF426GNY.bed.gz | 389.88 KB | 1e5fcc2ee908772bf420c685b5375859 |
| ENCFF426GNY.tabix.bed.gz | 348.61 KB | 77b673e120c68762656414662087486b |
| ENCFF426GNY.tabix.bed.gz.tbi | 221.55 KB | 2df175a0e5df745761435240cef7c83c |
| genomic_resource.yaml | 2.66 KB | 1fdfae8d87ca034248cc720354ee3b16 |
| statistics/ |