Resource
| Id | DNase-seq/ENCSR082JCE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR082JCE [biosample_summary="Homo sapiens kidney tissue female embryo (121 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (121 days) output_type: peaks audit_warning: Alignment file {ENCFF250ZEN|/files/ENCFF250ZEN/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 26118018 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 {ENCFF250ZEN|/files/ENCFF250ZEN/} 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_ENCSR082JCE | float |
DNase-seq_ENCSR082JCE |
DNase-seq ENCSR082JCE [biosample_summary="Homo sapiens kidney tissue female embryo (121 days)"]
|
 |
[0.308, 19.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7446765 | 0.23% | 42319 |
| chr1 | 677457 | 0.27% | 3846 |
| chr2 | 595618 | 0.25% | 3363 |
| chr3 | 481325 | 0.24% | 2747 |
| chr4 | 370439 | 0.19% | 2149 |
| chr5 | 412493 | 0.23% | 2351 |
| chr6 | 440380 | 0.26% | 2509 |
| chr7 | 370984 | 0.23% | 2149 |
| chr8 | 330724 | 0.23% | 1910 |
| chr9 | 311423 | 0.23% | 1761 |
| chr10 | 347938 | 0.26% | 1966 |
| chr11 | 391247 | 0.29% | 2210 |
| chr12 | 375376 | 0.28% | 2134 |
| chr13 | 186750 | 0.16% | 1066 |
| chr14 | 242238 | 0.23% | 1378 |
| chr15 | 234061 | 0.23% | 1333 |
| chr16 | 250901 | 0.28% | 1443 |
| chr17 | 307171 | 0.37% | 1709 |
| chr18 | 159376 | 0.20% | 952 |
| chr19 | 346334 | 0.59% | 1798 |
| chr20 | 198988 | 0.31% | 1160 |
| chr21 | 80708 | 0.17% | 458 |
| chr22 | 129314 | 0.25% | 727 |
| chrX | 205380 | 0.13% | 1199 |
| chrY | 140 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 42319 | 3 | 880 | 175.97 | 173 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF410WHC.bed.gz | 448.17 KB | ede7ecbf16d0318e2ef3c363bc32b517 |
| ENCFF410WHC.tabix.bed.gz | 396.19 KB | 86f69e8a9dbe6817c43b9b27c11c7d1b |
| ENCFF410WHC.tabix.bed.gz.tbi | 259.03 KB | 7b139291b9d418cb4ce82172d9c27ccf |
| genomic_resource.yaml | 2.65 KB | 998ce3ec8bd82a337ee090ff795ece11 |
| statistics/ |