Resource
| Id | DNase-seq/ENCSR092OFK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR092OFK [biosample_summary="Homo sapiens skin of body tissue female embryo (82 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (82 days) output_type: peaks audit_error: 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 {ENCFF198CSA|/files/ENCFF198CSA/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.19. 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/}) audit_internal_action: Released analysis {ENCAN037KSW|/analyses/ENCAN037KSW/} has in progress subobject document {90e895a1-4b12-47f5-a824-deaedc7048b1|/documents/90e895a1-4b12-47f5-a824-deaedc7048b1/} audit_warning: Alignment file {ENCFF198CSA|/files/ENCFF198CSA/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 32563147 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR092OFK | float |
DNase-seq_ENCSR092OFK |
DNase-seq ENCSR092OFK [biosample_summary="Homo sapiens skin of body tissue female embryo (82 days)"]
|
 |
[0.216, 18.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5921680 | 0.18% | 35958 |
| chr1 | 543170 | 0.22% | 3253 |
| chr2 | 475850 | 0.20% | 2934 |
| chr3 | 396104 | 0.20% | 2413 |
| chr4 | 315876 | 0.17% | 1944 |
| chr5 | 329312 | 0.18% | 2000 |
| chr6 | 353828 | 0.21% | 2189 |
| chr7 | 304286 | 0.19% | 1867 |
| chr8 | 272463 | 0.19% | 1697 |
| chr9 | 241088 | 0.17% | 1487 |
| chr10 | 273797 | 0.20% | 1677 |
| chr11 | 303690 | 0.22% | 1843 |
| chr12 | 297829 | 0.22% | 1795 |
| chr13 | 159140 | 0.14% | 950 |
| chr14 | 185718 | 0.17% | 1121 |
| chr15 | 184854 | 0.18% | 1115 |
| chr16 | 195674 | 0.22% | 1176 |
| chr17 | 227913 | 0.27% | 1364 |
| chr18 | 125329 | 0.16% | 795 |
| chr19 | 260841 | 0.44% | 1407 |
| chr20 | 145965 | 0.23% | 909 |
| chr21 | 64987 | 0.14% | 408 |
| chr22 | 94948 | 0.19% | 569 |
| chrX | 168718 | 0.11% | 1043 |
| chrY | 300 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 35958 | 6 | 780 | 164.68 | 160 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF950SDE.bed.gz | 374.32 KB | c15693638c1eb3003575345b0a32395e |
| ENCFF950SDE.tabix.bed.gz | 331.9 KB | 919621f2bf1a8bafbfd682ade3eb4e9b |
| ENCFF950SDE.tabix.bed.gz.tbi | 244.51 KB | 217e272bc105c9c45761cc27acc1c3b6 |
| genomic_resource.yaml | 2.87 KB | 2f3d78a10d0721c6d5bac8cf3378270c |
| statistics/ |