Resource
| Id | DNase-seq/ENCSR849OKE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR849OKE [biosample_summary="Homo sapiens renal cortex interstitium tissue male embryo (127 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (127 days) output_type: peaks audit_warning: Alignment file {ENCFF389PCQ|/files/ENCFF389PCQ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 38617784 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 {ENCFF389PCQ|/files/ENCFF389PCQ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.28. 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_ENCSR849OKE | float |
DNase-seq_ENCSR849OKE |
DNase-seq ENCSR849OKE [biosample_summary="Homo sapiens renal cortex interstitium tissue male embryo (127 days)"]
|
 |
[0.182, 12.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7685679 | 0.24% | 38919 |
| chr1 | 718917 | 0.29% | 3568 |
| chr2 | 602883 | 0.25% | 3114 |
| chr3 | 524338 | 0.26% | 2623 |
| chr4 | 382034 | 0.20% | 1987 |
| chr5 | 436085 | 0.24% | 2185 |
| chr6 | 494571 | 0.29% | 2440 |
| chr7 | 399423 | 0.25% | 2022 |
| chr8 | 331520 | 0.23% | 1713 |
| chr9 | 301776 | 0.22% | 1560 |
| chr10 | 358495 | 0.27% | 1855 |
| chr11 | 387292 | 0.29% | 1953 |
| chr12 | 384763 | 0.29% | 1936 |
| chr13 | 190305 | 0.17% | 958 |
| chr14 | 262129 | 0.24% | 1329 |
| chr15 | 257260 | 0.25% | 1302 |
| chr16 | 231754 | 0.26% | 1207 |
| chr17 | 309664 | 0.37% | 1559 |
| chr18 | 162085 | 0.20% | 816 |
| chr19 | 369730 | 0.63% | 1737 |
| chr20 | 186407 | 0.29% | 983 |
| chr21 | 83626 | 0.18% | 438 |
| chr22 | 121150 | 0.24% | 635 |
| chrX | 179512 | 0.12% | 953 |
| chrY | 9960 | 0.02% | 46 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 38919 | 1 | 960 | 197.48 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF746ACO.bed.gz | 397.72 KB | 6ef03a673f2a2313d77a57873f9c4042 |
| ENCFF746ACO.tabix.bed.gz | 360.4 KB | 2174325ad79ae2e7be99710e4ac08cc6 |
| ENCFF746ACO.tabix.bed.gz.tbi | 216.25 KB | a8e90e5904165c2f51dc80af215f53e8 |
| genomic_resource.yaml | 2.7 KB | 0b67ca562d9789578203c0416f392b3c |
| statistics/ |