Resource
| Id | DNase-seq/ENCSR282QFE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR282QFE [biosample_summary="Homo sapiens stomach tissue female embryo (121 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (121 days) output_type: peaks audit_warning: Alignment file {ENCFF343DHM|/files/ENCFF343DHM/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 31731786 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 {ENCFF343DHM|/files/ENCFF343DHM/} 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_ENCSR282QFE | float |
DNase-seq_ENCSR282QFE |
DNase-seq ENCSR282QFE [biosample_summary="Homo sapiens stomach tissue female embryo (121 days)"]
|
 |
[0.253, 16.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9703174 | 0.30% | 53853 |
| chr1 | 916012 | 0.37% | 5027 |
| chr2 | 765579 | 0.32% | 4287 |
| chr3 | 637844 | 0.32% | 3515 |
| chr4 | 469941 | 0.25% | 2645 |
| chr5 | 506180 | 0.28% | 2833 |
| chr6 | 598863 | 0.35% | 3270 |
| chr7 | 482290 | 0.30% | 2703 |
| chr8 | 423689 | 0.29% | 2391 |
| chr9 | 408017 | 0.29% | 2269 |
| chr10 | 445492 | 0.33% | 2495 |
| chr11 | 502821 | 0.37% | 2817 |
| chr12 | 490388 | 0.37% | 2729 |
| chr13 | 248180 | 0.22% | 1383 |
| chr14 | 320233 | 0.30% | 1761 |
| chr15 | 313941 | 0.31% | 1758 |
| chr16 | 314223 | 0.35% | 1762 |
| chr17 | 427385 | 0.51% | 2348 |
| chr18 | 205231 | 0.26% | 1162 |
| chr19 | 437558 | 0.75% | 2229 |
| chr20 | 245507 | 0.38% | 1387 |
| chr21 | 108951 | 0.23% | 621 |
| chr22 | 166861 | 0.33% | 937 |
| chrX | 267828 | 0.17% | 1523 |
| chrY | 160 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 53853 | 1 | 820 | 180.18 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF520NPY.bed.gz | 568.49 KB | cab24bcd9197462c91d03826d56a36e3 |
| ENCFF520NPY.tabix.bed.gz | 508.11 KB | 23c059be822ba390d460362b2a7ff858 |
| ENCFF520NPY.tabix.bed.gz.tbi | 297.5 KB | b81ce531332f07c6bb5d0c274af37270 |
| genomic_resource.yaml | 2.65 KB | 2199dfba4cd56b7db29b72b02daf1dc5 |
| statistics/ |