Resource
| Id | DNase-seq/ENCSR320SVK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR320SVK [biosample_summary="Homo sapiens left renal pelvis tissue male embryo (120 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (120 days) output_type: peaks audit_warning: Alignment file {ENCFF939OLN|/files/ENCFF939OLN/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 30452128 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 {ENCFF939OLN|/files/ENCFF939OLN/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR320SVK | float |
DNase-seq_ENCSR320SVK |
DNase-seq ENCSR320SVK [biosample_summary="Homo sapiens left renal pelvis tissue male embryo (120 days)"]
|
 |
[0.165, 18.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8202823 | 0.25% | 44951 |
| chr1 | 775023 | 0.31% | 4210 |
| chr2 | 630996 | 0.26% | 3479 |
| chr3 | 510395 | 0.26% | 2838 |
| chr4 | 405051 | 0.21% | 2251 |
| chr5 | 441454 | 0.24% | 2436 |
| chr6 | 519364 | 0.30% | 2793 |
| chr7 | 410790 | 0.26% | 2272 |
| chr8 | 370835 | 0.26% | 2037 |
| chr9 | 349024 | 0.25% | 1932 |
| chr10 | 390239 | 0.29% | 2174 |
| chr11 | 419739 | 0.31% | 2324 |
| chr12 | 414813 | 0.31% | 2265 |
| chr13 | 194119 | 0.17% | 1119 |
| chr14 | 274079 | 0.26% | 1478 |
| chr15 | 270750 | 0.27% | 1485 |
| chr16 | 272088 | 0.30% | 1502 |
| chr17 | 352695 | 0.42% | 1896 |
| chr18 | 172739 | 0.21% | 982 |
| chr19 | 391433 | 0.67% | 1956 |
| chr20 | 208277 | 0.32% | 1161 |
| chr21 | 90649 | 0.19% | 517 |
| chr22 | 142795 | 0.28% | 785 |
| chrX | 188919 | 0.12% | 1026 |
| chrY | 6557 | 0.01% | 33 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 44951 | 1 | 860 | 182.48 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF202LNA.bed.gz | 472.54 KB | cf720ce4f3df765c78d4167e83bf180f |
| ENCFF202LNA.tabix.bed.gz | 422.2 KB | 535425b0e45604c1df34524be3b0a9ae |
| ENCFF202LNA.tabix.bed.gz.tbi | 261.6 KB | 96625ce6ceb8b65400ed1a086660d448 |
| genomic_resource.yaml | 2.67 KB | deba10550f4664c8f5ec58026c02c362 |
| statistics/ |