Resource
| Id | DNase-seq/ENCSR389IHS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR389IHS [biosample_summary="Homo sapiens T-cell male adult (24 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (24 years) output_type: peaks audit_warning: Alignment file {ENCFF251CIK|/files/ENCFF251CIK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 41736008 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 {ENCFF251CIK|/files/ENCFF251CIK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.32. 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_ENCSR389IHS | float |
DNase-seq_ENCSR389IHS |
DNase-seq ENCSR389IHS [biosample_summary="Homo sapiens T-cell male adult (24 years)"]
|
 |
[0.241, 40.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5975519 | 0.19% | 32731 |
| chr1 | 609202 | 0.24% | 3321 |
| chr2 | 429584 | 0.18% | 2365 |
| chr3 | 338157 | 0.17% | 1881 |
| chr4 | 212301 | 0.11% | 1165 |
| chr5 | 273126 | 0.15% | 1508 |
| chr6 | 361547 | 0.21% | 1999 |
| chr7 | 276608 | 0.17% | 1509 |
| chr8 | 217824 | 0.15% | 1218 |
| chr9 | 230615 | 0.17% | 1270 |
| chr10 | 263399 | 0.20% | 1449 |
| chr11 | 300501 | 0.22% | 1644 |
| chr12 | 310786 | 0.23% | 1687 |
| chr13 | 120981 | 0.11% | 658 |
| chr14 | 211867 | 0.20% | 1166 |
| chr15 | 185942 | 0.18% | 1026 |
| chr16 | 243181 | 0.27% | 1331 |
| chr17 | 357380 | 0.43% | 1966 |
| chr18 | 93995 | 0.12% | 522 |
| chr19 | 399812 | 0.68% | 2105 |
| chr20 | 154843 | 0.24% | 865 |
| chr21 | 71161 | 0.15% | 391 |
| chr22 | 137608 | 0.27% | 749 |
| chrX | 165649 | 0.11% | 888 |
| chrY | 9450 | 0.02% | 48 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 32731 | 3 | 640 | 182.56 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF967SJS.bed.gz | 359.69 KB | fa8f60374128af4b171082f94dabed04 |
| ENCFF967SJS.tabix.bed.gz | 324.93 KB | b9def1cb29bfb39a3709c9a630366768 |
| ENCFF967SJS.tabix.bed.gz.tbi | 183.15 KB | 811bd24147b8216c90bb396a264a9d5a |
| genomic_resource.yaml | 2.62 KB | 81f3504a2d2718aff248b7ec3e9cb806 |
| statistics/ |