Resource
| Id | DNase-seq/ENCSR082XEU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR082XEU [biosample_summary="Homo sapiens stomach tissue female embryo (107 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (107 days) output_type: peaks audit_warning: Alignment file {ENCFF419VJY|/files/ENCFF419VJY/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 24638803 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 {ENCFF419VJY|/files/ENCFF419VJY/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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_ENCSR082XEU | float |
DNase-seq_ENCSR082XEU |
DNase-seq ENCSR082XEU [biosample_summary="Homo sapiens stomach tissue female embryo (107 days)"]
|
 |
[0.326, 15.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6669882 | 0.21% | 34311 |
| chr1 | 627437 | 0.25% | 3204 |
| chr2 | 513227 | 0.21% | 2629 |
| chr3 | 423210 | 0.21% | 2188 |
| chr4 | 325333 | 0.17% | 1641 |
| chr5 | 349956 | 0.19% | 1782 |
| chr6 | 412360 | 0.24% | 2087 |
| chr7 | 334896 | 0.21% | 1732 |
| chr8 | 273590 | 0.19% | 1457 |
| chr9 | 273123 | 0.20% | 1469 |
| chr10 | 296278 | 0.22% | 1570 |
| chr11 | 332169 | 0.25% | 1749 |
| chr12 | 358774 | 0.27% | 1831 |
| chr13 | 162314 | 0.14% | 828 |
| chr14 | 218921 | 0.20% | 1126 |
| chr15 | 230634 | 0.23% | 1187 |
| chr16 | 232216 | 0.26% | 1185 |
| chr17 | 297873 | 0.36% | 1531 |
| chr18 | 133117 | 0.17% | 710 |
| chr19 | 350651 | 0.60% | 1648 |
| chr20 | 156786 | 0.24% | 833 |
| chr21 | 72087 | 0.15% | 376 |
| chr22 | 119580 | 0.24% | 630 |
| chrX | 175210 | 0.11% | 917 |
| chrY | 140 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 34311 | 1 | 860 | 194.39 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF676PRF.bed.gz | 355.39 KB | ce0fbaec29d506fcd0c09b98a28db3ac |
| ENCFF676PRF.tabix.bed.gz | 319.91 KB | 736e8002073bae686e6ff369aae34b96 |
| ENCFF676PRF.tabix.bed.gz.tbi | 197.97 KB | a01042c3381486fcd43e49f9a4fb0476 |
| genomic_resource.yaml | 2.65 KB | 5976ebea499a3ca8668a82022f25f31c |
| statistics/ |