Resource
| Id | DNase-seq/ENCSR000EKF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EKF [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn"] |
| Description |
status: released biological_replicates: Rep 1 summary: newborn output_type: peaks audit_internal_action: Released analysis {ENCAN390QWY|/analyses/ENCAN390QWY/} has in progress subobject document {2f35d34b-ff7c-4790-b888-2a2f90a0ed0f|/documents/2f35d34b-ff7c-4790-b888-2a2f90a0ed0f/} audit_warning: Alignment file {ENCFF091KTX|/files/ENCFF091KTX/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 28233440 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 {ENCFF091KTX|/files/ENCFF091KTX/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) 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-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000EKF | float |
DNase-seq_ENCSR000EKF |
DNase-seq ENCSR000EKF [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn"]
|
 |
[0.291, 19.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8088772 | 0.25% | 46576 |
| chr1 | 775041 | 0.31% | 4466 |
| chr2 | 603624 | 0.25% | 3508 |
| chr3 | 477893 | 0.24% | 2788 |
| chr4 | 357265 | 0.19% | 2074 |
| chr5 | 394636 | 0.22% | 2275 |
| chr6 | 431439 | 0.25% | 2503 |
| chr7 | 429363 | 0.27% | 2473 |
| chr8 | 340370 | 0.23% | 1992 |
| chr9 | 355637 | 0.26% | 2021 |
| chr10 | 370841 | 0.28% | 2161 |
| chr11 | 434719 | 0.32% | 2513 |
| chr12 | 399708 | 0.30% | 2323 |
| chr13 | 199651 | 0.17% | 1182 |
| chr14 | 251529 | 0.23% | 1426 |
| chr15 | 275906 | 0.27% | 1583 |
| chr16 | 324107 | 0.36% | 1841 |
| chr17 | 410302 | 0.49% | 2330 |
| chr18 | 175414 | 0.22% | 1022 |
| chr19 | 441708 | 0.75% | 2392 |
| chr20 | 226409 | 0.35% | 1303 |
| chr21 | 103057 | 0.22% | 569 |
| chr22 | 180877 | 0.36% | 1027 |
| chrX | 125878 | 0.08% | 785 |
| chrY | 3398 | 0.01% | 19 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 46576 | 2 | 780 | 173.67 | 170 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF833UNB.bed.gz | 486.6 KB | e5b8cba744aae4f6295600234b037dc8 |
| ENCFF833UNB.tabix.bed.gz | 432.82 KB | 0c0a2135822484382543907be7094d53 |
| ENCFF833UNB.tabix.bed.gz.tbi | 255.49 KB | 2dfb2dcb529fa76cc2df36ade0c3dcb4 |
| genomic_resource.yaml | 2.99 KB | 2f638858edc5d6a5e6d041cdef996c9b |
| statistics/ |