Resource
| Id | DNase-seq/ENCSR178JBL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR178JBL [biosample_summary="Homo sapiens pancreas tissue male adult (34 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: peaks audit_warning: Alignment file {ENCFF074OHR|/files/ENCFF074OHR/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 38206997 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 {ENCFF074OHR|/files/ENCFF074OHR/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.29. 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_ENCSR178JBL | float |
DNase-seq_ENCSR178JBL |
DNase-seq ENCSR178JBL [biosample_summary="Homo sapiens pancreas tissue male adult (34 years)"]
|
 |
[0.158, 29.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9396360 | 0.29% | 51238 |
| chr1 | 929895 | 0.37% | 5033 |
| chr2 | 745194 | 0.31% | 4075 |
| chr3 | 612094 | 0.31% | 3387 |
| chr4 | 435185 | 0.23% | 2388 |
| chr5 | 489763 | 0.27% | 2715 |
| chr6 | 549961 | 0.32% | 3029 |
| chr7 | 486020 | 0.31% | 2685 |
| chr8 | 426132 | 0.29% | 2346 |
| chr9 | 394914 | 0.29% | 2166 |
| chr10 | 448293 | 0.34% | 2504 |
| chr11 | 488468 | 0.36% | 2656 |
| chr12 | 476621 | 0.36% | 2608 |
| chr13 | 225129 | 0.20% | 1227 |
| chr14 | 315708 | 0.29% | 1716 |
| chr15 | 316026 | 0.31% | 1700 |
| chr16 | 319081 | 0.35% | 1696 |
| chr17 | 416475 | 0.50% | 2201 |
| chr18 | 198436 | 0.25% | 1119 |
| chr19 | 399340 | 0.68% | 2035 |
| chr20 | 229543 | 0.36% | 1254 |
| chr21 | 96540 | 0.21% | 535 |
| chr22 | 175106 | 0.34% | 955 |
| chrX | 211345 | 0.14% | 1140 |
| chrY | 11091 | 0.02% | 68 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 51238 | 13 | 780 | 183.39 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF118OAK.bed.gz | 542.37 KB | 2ed2d3c6625cb67b3b562efb87349051 |
| ENCFF118OAK.tabix.bed.gz | 486.83 KB | dc402bb0f89c8e1fb5a577976606d283 |
| ENCFF118OAK.tabix.bed.gz.tbi | 291.97 KB | 9a3aa2f9c5e95c624513074f810d567a |
| genomic_resource.yaml | 2.64 KB | aa5152a0ef36f036ae3ec85d6337ba9d |
| statistics/ |