Resource
| Id | DNase-seq/ENCSR956ZHU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR956ZHU [biosample_summary="Homo sapiens renal pelvis tissue male embryo (113 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (113 days) output_type: peaks audit_warning: Alignment file {ENCFF246LGF|/files/ENCFF246LGF/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 34793316 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 {ENCFF246LGF|/files/ENCFF246LGF/} 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_ENCSR956ZHU | float |
DNase-seq_ENCSR956ZHU |
DNase-seq ENCSR956ZHU [biosample_summary="Homo sapiens renal pelvis tissue male embryo (113 days)"]
|
 |
[0.231, 21.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9296238 | 0.29% | 48045 |
| chr1 | 881243 | 0.35% | 4515 |
| chr2 | 741738 | 0.31% | 3862 |
| chr3 | 603920 | 0.30% | 3097 |
| chr4 | 457346 | 0.24% | 2398 |
| chr5 | 517251 | 0.28% | 2698 |
| chr6 | 553807 | 0.32% | 2834 |
| chr7 | 459162 | 0.29% | 2393 |
| chr8 | 404750 | 0.28% | 2157 |
| chr9 | 384015 | 0.28% | 2001 |
| chr10 | 428315 | 0.32% | 2267 |
| chr11 | 477358 | 0.35% | 2472 |
| chr12 | 486955 | 0.37% | 2465 |
| chr13 | 239570 | 0.21% | 1253 |
| chr14 | 303152 | 0.28% | 1540 |
| chr15 | 302717 | 0.30% | 1576 |
| chr16 | 303481 | 0.34% | 1588 |
| chr17 | 391492 | 0.47% | 1997 |
| chr18 | 204064 | 0.25% | 1068 |
| chr19 | 424832 | 0.72% | 2037 |
| chr20 | 243105 | 0.38% | 1298 |
| chr21 | 101358 | 0.22% | 532 |
| chr22 | 160460 | 0.32% | 840 |
| chrX | 218784 | 0.14% | 1123 |
| chrY | 7363 | 0.01% | 34 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 48045 | 1 | 1020 | 193.49 | 181 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF474VCE.bed.gz | 506.54 KB | bc3dea9c34f47cbcfa953ed89f25fb17 |
| ENCFF474VCE.tabix.bed.gz | 454.15 KB | 3ab8a3cc286519ec87453acf892cd5f8 |
| ENCFF474VCE.tabix.bed.gz.tbi | 266.34 KB | badcb38cddf12aeba19908de170a04f3 |
| genomic_resource.yaml | 2.66 KB | f4e3b9afc6305a2ed563c5070c35ed59 |
| statistics/ |