Resource
| Id | DNase-seq/ENCSR000ENX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000ENX [biosample_summary="Homo sapiens dermis blood vessel endothelial cell female adult"] |
| Description |
status: released biological_replicates: Rep 2 summary: female adult output_type: peaks audit_error: 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 {ENCFF807STB|/files/ENCFF807STB/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.19. 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: Alignment file {ENCFF409JXE|/files/ENCFF409JXE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 24707781 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: Alignment file {ENCFF807STB|/files/ENCFF807STB/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 33364789 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 {ENCFF409JXE|/files/ENCFF409JXE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 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_ENCSR000ENX | float |
DNase-seq_ENCSR000ENX |
DNase-seq ENCSR000ENX [biosample_summary="Homo sapiens dermis blood vessel endothelial cell female adult"]
|
 |
[0.271, 14.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6086608 | 0.19% | 34287 |
| chr1 | 560817 | 0.23% | 3174 |
| chr2 | 468766 | 0.19% | 2627 |
| chr3 | 407116 | 0.21% | 2294 |
| chr4 | 295806 | 0.16% | 1686 |
| chr5 | 330791 | 0.18% | 1906 |
| chr6 | 375100 | 0.22% | 2115 |
| chr7 | 307376 | 0.19% | 1772 |
| chr8 | 270221 | 0.19% | 1528 |
| chr9 | 249118 | 0.18% | 1405 |
| chr10 | 279084 | 0.21% | 1574 |
| chr11 | 291382 | 0.22% | 1614 |
| chr12 | 341720 | 0.26% | 1928 |
| chr13 | 169232 | 0.15% | 962 |
| chr14 | 187326 | 0.17% | 1045 |
| chr15 | 206540 | 0.20% | 1170 |
| chr16 | 198638 | 0.22% | 1131 |
| chr17 | 260517 | 0.31% | 1447 |
| chr18 | 121969 | 0.15% | 698 |
| chr19 | 277208 | 0.47% | 1457 |
| chr20 | 156302 | 0.24% | 883 |
| chr21 | 70624 | 0.15% | 385 |
| chr22 | 109595 | 0.22% | 611 |
| chrX | 150952 | 0.10% | 872 |
| chrY | 408 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 34287 | 16 | 600 | 177.52 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF609ZYN.bed.gz | 361.95 KB | 82190d8647b48470c37b5a06fae58f55 |
| ENCFF609ZYN.tabix.bed.gz | 323.22 KB | 6c424ba27144a97f417165edb221c273 |
| ENCFF609ZYN.tabix.bed.gz.tbi | 214.26 KB | b9f489f05f51b79ce9adc1b2df104ae8 |
| genomic_resource.yaml | 4.1 KB | 5b8adf2dfea49cd560d518aa738124ac |
| statistics/ |