Resource
| Id | DNase-seq/ENCSR620WAR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR620WAR [biosample_summary="Homo sapiens SJSA1"] |
| Description |
status: released biological_replicates: Rep 2 summary: output_type: peaks audit_warning: Alignment file {ENCFF255DYN|/files/ENCFF255DYN/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 40698671 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 {ENCFF255DYN|/files/ENCFF255DYN/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR620WAR | float |
DNase-seq_ENCSR620WAR |
DNase-seq ENCSR620WAR [biosample_summary="Homo sapiens SJSA1"]
|
 |
[0.0274, 189] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 38227351 | 1.19% | 154549 |
| chr1 | 3428239 | 1.38% | 13780 |
| chr2 | 3117015 | 1.29% | 12564 |
| chr3 | 2329014 | 1.17% | 9571 |
| chr4 | 1821126 | 0.96% | 7476 |
| chr5 | 2324786 | 1.28% | 9215 |
| chr6 | 2453698 | 1.44% | 9779 |
| chr7 | 1888628 | 1.19% | 7715 |
| chr8 | 1808787 | 1.25% | 7336 |
| chr9 | 1464880 | 1.06% | 5902 |
| chr10 | 1801194 | 1.35% | 7346 |
| chr11 | 1672203 | 1.24% | 6963 |
| chr12 | 2875705 | 2.16% | 10918 |
| chr13 | 1098344 | 0.96% | 4452 |
| chr14 | 1057641 | 0.99% | 4351 |
| chr15 | 1287796 | 1.26% | 5190 |
| chr16 | 1192842 | 1.32% | 4872 |
| chr17 | 1621856 | 1.95% | 6616 |
| chr18 | 867544 | 1.08% | 3497 |
| chr19 | 1054118 | 1.80% | 4380 |
| chr20 | 903324 | 1.40% | 3688 |
| chr21 | 466610 | 1.00% | 1857 |
| chr22 | 655569 | 1.29% | 2683 |
| chrX | 978175 | 0.63% | 4150 |
| chrY | 58257 | 0.10% | 248 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 154549 | 1 | 1540 | 247.35 | 240 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF319DRN.bed.gz | 1.6 MB | b8f11b3a717a4ae8d0b6b7cc76506bcf |
| ENCFF319DRN.tabix.bed.gz | 1.51 MB | 42ab2756b72519df4c42487a55645cf2 |
| ENCFF319DRN.tabix.bed.gz.tbi | 480.95 KB | 371f373e40c4d531d98d4c8a9a087285 |
| genomic_resource.yaml | 2.55 KB | 55d365001b2468dcc0e208d3242e3cc7 |
| statistics/ |