Resource
| Id | DNase-seq/ENCSR000EOQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EOQ [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn"] |
| Description |
status: released biological_replicates: Rep 1 summary: newborn output_type: peaks audit_warning: Alignment file {ENCFF400NFM|/files/ENCFF400NFM/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 31477814 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 {ENCFF400NFM|/files/ENCFF400NFM/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.30. 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/}) 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 {ENCFF374GNN|/files/ENCFF374GNN/} 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_ENCSR000EOQ | float |
DNase-seq_ENCSR000EOQ |
DNase-seq ENCSR000EOQ [biosample_summary="Homo sapiens endothelial cell of umbilical vein newborn"]
|
 |
[0.0196, 22.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 42918118 | 1.33% | 178342 |
| chr1 | 3913156 | 1.57% | 16175 |
| chr2 | 3542513 | 1.46% | 14740 |
| chr3 | 2977017 | 1.50% | 12192 |
| chr4 | 2359566 | 1.24% | 9692 |
| chr5 | 2483395 | 1.37% | 10193 |
| chr6 | 2757139 | 1.61% | 11186 |
| chr7 | 2253641 | 1.41% | 9375 |
| chr8 | 2017206 | 1.39% | 8253 |
| chr9 | 1814283 | 1.31% | 7578 |
| chr10 | 2040738 | 1.53% | 8420 |
| chr11 | 2031660 | 1.50% | 8546 |
| chr12 | 2290183 | 1.72% | 9495 |
| chr13 | 1293838 | 1.13% | 5284 |
| chr14 | 1342477 | 1.25% | 5553 |
| chr15 | 1440016 | 1.41% | 5910 |
| chr16 | 1170197 | 1.30% | 5103 |
| chr17 | 1633080 | 1.96% | 6917 |
| chr18 | 971476 | 1.21% | 4009 |
| chr19 | 1056529 | 1.80% | 4636 |
| chr20 | 1027138 | 1.59% | 4322 |
| chr21 | 487490 | 1.04% | 2020 |
| chr22 | 631230 | 1.24% | 2758 |
| chrX | 1323753 | 0.85% | 5700 |
| chrY | 60397 | 0.11% | 285 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 178342 | 1 | 1300 | 240.65 | 231 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF080VVT.bed.gz | 1.9 MB | e68283fe7c73626e0459f97ec4c27fa8 |
| ENCFF080VVT.tabix.bed.gz | 1.76 MB | 0630fd9cb4fd5f1e854c4478da2aee68 |
| ENCFF080VVT.tabix.bed.gz.tbi | 532.59 KB | 87d399b602aca76637aaf155268a0baf |
| genomic_resource.yaml | 3.62 KB | 37a1b5daf1cac6a2a7cefd00422d3065 |
| statistics/ |