Resource
| Id | DNase-seq/ENCSR564TUY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR564TUY [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive male"] |
| Description |
status: released biological_replicates: Rep 1 summary: male output_type: peaks audit_warning: Alignment file {ENCFF917PBO|/files/ENCFF917PBO/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 34425185 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 {ENCFF917PBO|/files/ENCFF917PBO/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR564TUY | float |
DNase-seq_ENCSR564TUY |
DNase-seq ENCSR564TUY [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive male"]
|
 |
[0.263, 36.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 13046480 | 0.41% | 73719 |
| chr1 | 1236114 | 0.50% | 6971 |
| chr2 | 1015606 | 0.42% | 5818 |
| chr3 | 863207 | 0.44% | 4882 |
| chr4 | 630394 | 0.33% | 3617 |
| chr5 | 678109 | 0.37% | 3854 |
| chr6 | 786610 | 0.46% | 4465 |
| chr7 | 664081 | 0.42% | 3794 |
| chr8 | 576258 | 0.40% | 3301 |
| chr9 | 527822 | 0.38% | 3020 |
| chr10 | 627233 | 0.47% | 3581 |
| chr11 | 637387 | 0.47% | 3580 |
| chr12 | 653845 | 0.49% | 3656 |
| chr13 | 346863 | 0.30% | 1978 |
| chr14 | 431219 | 0.40% | 2446 |
| chr15 | 417437 | 0.41% | 2358 |
| chr16 | 417007 | 0.46% | 2309 |
| chr17 | 582056 | 0.70% | 3243 |
| chr18 | 270793 | 0.34% | 1553 |
| chr19 | 558361 | 0.95% | 2941 |
| chr20 | 348386 | 0.54% | 1994 |
| chr21 | 162110 | 0.35% | 916 |
| chr22 | 248873 | 0.49% | 1392 |
| chrX | 350456 | 0.22% | 1962 |
| chrY | 16253 | 0.03% | 88 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 73719 | 20 | 900 | 176.98 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF329LXI.bed.gz | 784.77 KB | 90d5a234a8343fdc42a0269ddfbe8870 |
| ENCFF329LXI.tabix.bed.gz | 703.66 KB | 3ead00c860cdd45862e1081b3a5c0fcb |
| ENCFF329LXI.tabix.bed.gz.tbi | 378.13 KB | 7519a06914577f29fede7e05f103639d |
| genomic_resource.yaml | 2.63 KB | 8feb39d861906ca3280b5456f69901ee |
| statistics/ |