Resource
| Id | DNase-seq/ENCSR328UMC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR328UMC [biosample_summary="Homo sapiens hematopoietic multipotent progenitor cell"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (34 years) output_type: peaks audit_internal_action: Archived analysis {ENCAN958FFS|/analyses/ENCAN958FFS/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF128IGS|/files/ENCFF128IGS/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 30858301 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/}) audit_warning: Alignment file {ENCFF993CDV|/files/ENCFF993CDV/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 30588883 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/}) 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 {ENCFF993CDV|/files/ENCFF993CDV/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR328UMC | float |
DNase-seq_ENCSR328UMC |
DNase-seq ENCSR328UMC [biosample_summary="Homo sapiens hematopoietic multipotent progenitor cell"]
|
 |
[3, 1.31e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6606556 | 0.21% | 43906 |
| chr1 | 656139 | 0.26% | 4361 |
| chr2 | 474767 | 0.20% | 3162 |
| chr3 | 379365 | 0.19% | 2521 |
| chr4 | 264233 | 0.14% | 1756 |
| chr5 | 315880 | 0.17% | 2095 |
| chr6 | 406016 | 0.24% | 2690 |
| chr7 | 310281 | 0.19% | 2064 |
| chr8 | 255589 | 0.18% | 1699 |
| chr9 | 260563 | 0.19% | 1733 |
| chr10 | 300481 | 0.22% | 1993 |
| chr11 | 341244 | 0.25% | 2271 |
| chr12 | 343217 | 0.26% | 2284 |
| chr13 | 140795 | 0.12% | 937 |
| chr14 | 222551 | 0.21% | 1477 |
| chr15 | 207746 | 0.20% | 1375 |
| chr16 | 256241 | 0.28% | 1703 |
| chr17 | 365793 | 0.44% | 2434 |
| chr18 | 109772 | 0.14% | 728 |
| chr19 | 366455 | 0.63% | 2444 |
| chr20 | 182672 | 0.28% | 1214 |
| chr21 | 81750 | 0.18% | 544 |
| chr22 | 143663 | 0.28% | 957 |
| chrX | 219693 | 0.14% | 1454 |
| chrY | 1650 | <0.01% | 10 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 43906 | 21 | 343 | 150.47 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF626VVB.bed.gz | 430.56 KB | 2b5b0bd6e3c2af38fe5355332620429b |
| ENCFF626VVB.tabix.bed.gz | 371.54 KB | e2425e8767f34775706f0355999e2461 |
| ENCFF626VVB.tabix.bed.gz.tbi | 228.67 KB | e297b62b53421d36b581b4fe942c386d |
| genomic_resource.yaml | 3.41 KB | 90ae69d574b2d5b9e2219f3c65072d21 |
| statistics/ |