Resource
| Id | DNase-seq/ENCSR129GCL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR129GCL [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 {ENCFF012FEK|/files/ENCFF012FEK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 35688072 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 {ENCFF012FEK|/files/ENCFF012FEK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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_ENCSR129GCL | float |
DNase-seq_ENCSR129GCL |
DNase-seq ENCSR129GCL [biosample_summary="Homo sapiens CD4-positive, alpha-beta T cell male adult (42 years)"]
|
 |
[0.365, 37.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6071329 | 0.19% | 33188 |
| chr1 | 628251 | 0.25% | 3444 |
| chr2 | 414990 | 0.17% | 2280 |
| chr3 | 327381 | 0.17% | 1789 |
| chr4 | 203377 | 0.11% | 1118 |
| chr5 | 264710 | 0.15% | 1450 |
| chr6 | 341083 | 0.20% | 1903 |
| chr7 | 280987 | 0.18% | 1544 |
| chr8 | 217083 | 0.15% | 1215 |
| chr9 | 243955 | 0.18% | 1340 |
| chr10 | 254864 | 0.19% | 1394 |
| chr11 | 326090 | 0.24% | 1773 |
| chr12 | 317278 | 0.24% | 1730 |
| chr13 | 119149 | 0.10% | 634 |
| chr14 | 213855 | 0.20% | 1159 |
| chr15 | 193237 | 0.19% | 1064 |
| chr16 | 248138 | 0.27% | 1343 |
| chr17 | 387572 | 0.47% | 2110 |
| chr18 | 89903 | 0.11% | 492 |
| chr19 | 435014 | 0.74% | 2284 |
| chr20 | 167741 | 0.26% | 937 |
| chr21 | 72811 | 0.16% | 400 |
| chr22 | 149035 | 0.29% | 827 |
| chrX | 167591 | 0.11% | 918 |
| chrY | 7234 | 0.01% | 40 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 33188 | 2 | 680 | 182.94 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF859OCM.bed.gz | 364.46 KB | ccfb9a2a60cc06a32375cda4c1e8b2bc |
| ENCFF859OCM.tabix.bed.gz | 330.13 KB | e258e3e2ba417ec7ca2905fc3f6b6b33 |
| ENCFF859OCM.tabix.bed.gz.tbi | 187.1 KB | 01e46024e38c21231585f7292d13d48e |
| genomic_resource.yaml | 2.7 KB | 25f94097d41bb2c33df3e7722724ca1c |
| statistics/ |