Resource
| Id | DNase-seq/ENCSR281HBB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR281HBB [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive male adult (49 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (49 years) output_type: peaks audit_internal_action: Archived analysis {ENCAN534XXT|/analyses/ENCAN534XXT/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF265ZUN|/files/ENCFF265ZUN/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 35318388 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 {ENCFF672QYE|/files/ENCFF672QYE/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 35004897 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 {ENCFF672QYE|/files/ENCFF672QYE/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.40. 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_ENCSR281HBB | float |
DNase-seq_ENCSR281HBB |
DNase-seq ENCSR281HBB [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive male adult (49 years)"]
|
 |
[4, 4.93e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 13259786 | 0.41% | 88297 |
| chr1 | 1236150 | 0.50% | 8227 |
| chr2 | 1027272 | 0.42% | 6841 |
| chr3 | 862050 | 0.43% | 5740 |
| chr4 | 631800 | 0.33% | 4210 |
| chr5 | 703894 | 0.39% | 4682 |
| chr6 | 803925 | 0.47% | 5354 |
| chr7 | 671685 | 0.42% | 4471 |
| chr8 | 599550 | 0.41% | 3994 |
| chr9 | 535742 | 0.39% | 3571 |
| chr10 | 633392 | 0.47% | 4219 |
| chr11 | 641693 | 0.48% | 4276 |
| chr12 | 666900 | 0.50% | 4441 |
| chr13 | 349947 | 0.31% | 2329 |
| chr14 | 428100 | 0.40% | 2852 |
| chr15 | 429342 | 0.42% | 2860 |
| chr16 | 430350 | 0.48% | 2865 |
| chr17 | 595723 | 0.72% | 3968 |
| chr18 | 284850 | 0.35% | 1894 |
| chr19 | 548951 | 0.94% | 3659 |
| chr20 | 347920 | 0.54% | 2317 |
| chr21 | 159000 | 0.34% | 1059 |
| chr22 | 247650 | 0.49% | 1648 |
| chrX | 401250 | 0.26% | 2669 |
| chrY | 22650 | 0.04% | 151 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 88297 | 42 | 300 | 150.17 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF111XGH.bed.gz | 856.35 KB | b8207d2f78b19638f25a57896d9ed84d |
| ENCFF111XGH.tabix.bed.gz | 741.34 KB | 168d4a2e8f161c7371cde30efbaea559 |
| ENCFF111XGH.tabix.bed.gz.tbi | 428.0 KB | bb445dcc59c33a89e1a17542059d243c |
| genomic_resource.yaml | 3.46 KB | 900b3b6748a75f2ae30bcdbc48828f0a |
| statistics/ |