Resource
| Id | DNase-seq/ENCSR986HEN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR986HEN [biosample_summary="Homo sapiens right renal pelvis tissue male embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (105 days) output_type: peaks audit_warning: Alignment file {ENCFF288NSD|/files/ENCFF288NSD/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 30365668 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 {ENCFF288NSD|/files/ENCFF288NSD/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR986HEN | float |
DNase-seq_ENCSR986HEN |
DNase-seq ENCSR986HEN [biosample_summary="Homo sapiens right renal pelvis tissue male embryo (105 days)"]
|
 |
[0.265, 16.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9037173 | 0.28% | 51570 |
| chr1 | 822564 | 0.33% | 4664 |
| chr2 | 708771 | 0.29% | 4064 |
| chr3 | 587512 | 0.30% | 3367 |
| chr4 | 460245 | 0.24% | 2641 |
| chr5 | 504034 | 0.28% | 2873 |
| chr6 | 547695 | 0.32% | 3106 |
| chr7 | 443413 | 0.28% | 2577 |
| chr8 | 400870 | 0.28% | 2295 |
| chr9 | 384004 | 0.28% | 2199 |
| chr10 | 434275 | 0.32% | 2517 |
| chr11 | 470887 | 0.35% | 2706 |
| chr12 | 449265 | 0.34% | 2545 |
| chr13 | 234286 | 0.20% | 1339 |
| chr14 | 294033 | 0.27% | 1645 |
| chr15 | 290982 | 0.29% | 1672 |
| chr16 | 301522 | 0.33% | 1726 |
| chr17 | 368599 | 0.44% | 2105 |
| chr18 | 206720 | 0.26% | 1222 |
| chr19 | 401164 | 0.68% | 2121 |
| chr20 | 244168 | 0.38% | 1414 |
| chr21 | 102706 | 0.22% | 595 |
| chr22 | 158479 | 0.31% | 915 |
| chrX | 214569 | 0.14% | 1228 |
| chrY | 6410 | 0.01% | 34 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 51570 | 1 | 800 | 175.24 | 170 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF581IEQ.bed.gz | 542.03 KB | 85540114b4f66817d3c77a6cf5f5dab1 |
| ENCFF581IEQ.tabix.bed.gz | 482.0 KB | 0a275ff996238979b0bdc5f747b7272b |
| ENCFF581IEQ.tabix.bed.gz.tbi | 296.47 KB | 9b452a69ca2e34d4fe94c5c6779d0d95 |
| genomic_resource.yaml | 2.68 KB | 1b02b4973583dc49d1f4bc5bd774f4bb |
| statistics/ |