Resource
| Id | DNase-seq/ENCSR709YRE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR709YRE [biosample_summary="Homo sapiens T-helper 17 cell male adult (42 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (42 years) output_type: peaks audit_warning: Alignment file {ENCFF520CBX|/files/ENCFF520CBX/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 45344668 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 {ENCFF520CBX|/files/ENCFF520CBX/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.35. 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_ENCSR709YRE | float |
DNase-seq_ENCSR709YRE |
DNase-seq ENCSR709YRE [biosample_summary="Homo sapiens T-helper 17 cell male adult (42 years)"]
|
 |
[0.221, 27.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7162142 | 0.22% | 37233 |
| chr1 | 733426 | 0.29% | 3808 |
| chr2 | 495636 | 0.20% | 2614 |
| chr3 | 398666 | 0.20% | 2079 |
| chr4 | 242526 | 0.13% | 1288 |
| chr5 | 318077 | 0.18% | 1673 |
| chr6 | 439986 | 0.26% | 2265 |
| chr7 | 331304 | 0.21% | 1733 |
| chr8 | 266949 | 0.18% | 1387 |
| chr9 | 279942 | 0.20% | 1460 |
| chr10 | 305171 | 0.23% | 1604 |
| chr11 | 368248 | 0.27% | 1917 |
| chr12 | 385891 | 0.29% | 1992 |
| chr13 | 145089 | 0.13% | 742 |
| chr14 | 247321 | 0.23% | 1276 |
| chr15 | 231328 | 0.23% | 1215 |
| chr16 | 299865 | 0.33% | 1535 |
| chr17 | 435578 | 0.52% | 2254 |
| chr18 | 111901 | 0.14% | 582 |
| chr19 | 480705 | 0.82% | 2410 |
| chr20 | 192178 | 0.30% | 1028 |
| chr21 | 79661 | 0.17% | 420 |
| chr22 | 175794 | 0.35% | 912 |
| chrX | 188577 | 0.12% | 998 |
| chrY | 8323 | 0.01% | 41 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 37233 | 7 | 700 | 192.36 | 181 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF589UWU.bed.gz | 406.84 KB | 57b17eee5811b17f6c2a45a5aea76865 |
| ENCFF589UWU.tabix.bed.gz | 368.28 KB | e538f8c4234b791144ac553ac50fda32 |
| ENCFF589UWU.tabix.bed.gz.tbi | 199.49 KB | 6a31b032aacd84ba5cf99ff3c0a6667a |
| genomic_resource.yaml | 2.65 KB | d596ecd2575ea50aa9cbec3756edb005 |
| statistics/ |