Resource
| Id | DNase-seq/ENCSR240TZG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR240TZG [biosample_summary="Homo sapiens CD4-positive, alpha-beta T cell male adult (42 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (42 years) output_type: peaks audit_warning: Alignment file {ENCFF862ZLM|/files/ENCFF862ZLM/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 47145902 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 {ENCFF862ZLM|/files/ENCFF862ZLM/} 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_ENCSR240TZG | float |
DNase-seq_ENCSR240TZG |
DNase-seq ENCSR240TZG [biosample_summary="Homo sapiens CD4-positive, alpha-beta T cell male adult (42 years)"]
|
 |
[0.192, 28.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6312135 | 0.20% | 33966 |
| chr1 | 651807 | 0.26% | 3510 |
| chr2 | 428953 | 0.18% | 2333 |
| chr3 | 340512 | 0.17% | 1820 |
| chr4 | 212608 | 0.11% | 1151 |
| chr5 | 274213 | 0.15% | 1468 |
| chr6 | 357073 | 0.21% | 1907 |
| chr7 | 284492 | 0.18% | 1534 |
| chr8 | 222625 | 0.15% | 1228 |
| chr9 | 252258 | 0.18% | 1367 |
| chr10 | 267147 | 0.20% | 1445 |
| chr11 | 333735 | 0.25% | 1791 |
| chr12 | 327725 | 0.25% | 1766 |
| chr13 | 123828 | 0.11% | 655 |
| chr14 | 221184 | 0.21% | 1189 |
| chr15 | 207829 | 0.20% | 1121 |
| chr16 | 269658 | 0.30% | 1443 |
| chr17 | 400182 | 0.48% | 2165 |
| chr18 | 91527 | 0.11% | 504 |
| chr19 | 456134 | 0.78% | 2374 |
| chr20 | 172653 | 0.27% | 938 |
| chr21 | 73618 | 0.16% | 410 |
| chr22 | 157226 | 0.31% | 849 |
| chrX | 177790 | 0.11% | 961 |
| chrY | 7358 | 0.01% | 37 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 33966 | 17 | 640 | 185.84 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF835RUA.bed.gz | 372.18 KB | 8f67b120b3180bd3b871a5e3cddc12d9 |
| ENCFF835RUA.tabix.bed.gz | 338.29 KB | 67e7a000db34c3002e3128a9c838eed7 |
| ENCFF835RUA.tabix.bed.gz.tbi | 189.89 KB | c3acc882dbd337966f592f92d4b9b4a9 |
| genomic_resource.yaml | 2.7 KB | 03ec4d67c6abce1a9f0cd80c552aeb0b |
| statistics/ |