Resource
| Id | DNase-seq/ENCSR014VAC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR014VAC [biosample_summary="Homo sapiens right renal cortex interstitium tissue male embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (105 days) output_type: peaks audit_warning: Alignment file {ENCFF203UES|/files/ENCFF203UES/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 37127546 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 {ENCFF203UES|/files/ENCFF203UES/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.26. 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_ENCSR014VAC | float |
DNase-seq_ENCSR014VAC |
DNase-seq ENCSR014VAC [biosample_summary="Homo sapiens right renal cortex interstitium tissue male embryo (105 days)"]
|
 |
[0.216, 10.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6620671 | 0.21% | 33920 |
| chr1 | 628041 | 0.25% | 3146 |
| chr2 | 520401 | 0.21% | 2695 |
| chr3 | 442213 | 0.22% | 2280 |
| chr4 | 349058 | 0.18% | 1811 |
| chr5 | 375135 | 0.21% | 1903 |
| chr6 | 443710 | 0.26% | 2222 |
| chr7 | 327421 | 0.21% | 1683 |
| chr8 | 278061 | 0.19% | 1481 |
| chr9 | 269387 | 0.19% | 1407 |
| chr10 | 291483 | 0.22% | 1546 |
| chr11 | 345740 | 0.26% | 1758 |
| chr12 | 340443 | 0.26% | 1726 |
| chr13 | 170702 | 0.15% | 886 |
| chr14 | 214069 | 0.20% | 1058 |
| chr15 | 217070 | 0.21% | 1100 |
| chr16 | 206475 | 0.23% | 1086 |
| chr17 | 261621 | 0.31% | 1349 |
| chr18 | 139560 | 0.17% | 748 |
| chr19 | 317243 | 0.54% | 1448 |
| chr20 | 158978 | 0.25% | 859 |
| chr21 | 68836 | 0.15% | 367 |
| chr22 | 98379 | 0.19% | 530 |
| chrX | 150449 | 0.10% | 804 |
| chrY | 6196 | 0.01% | 27 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 33920 | 1 | 952 | 195.18 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF056EMK.bed.gz | 348.72 KB | 2bf91aceb53872de988406cda99c14d8 |
| ENCFF056EMK.tabix.bed.gz | 313.9 KB | 59e9be02b46f189856ca6f6ac1d7e9e2 |
| ENCFF056EMK.tabix.bed.gz.tbi | 199.53 KB | d831394cfa2444ba4427221a5ed76302 |
| genomic_resource.yaml | 2.72 KB | b221d2158bbf5ced992a9234d8ba8fb8 |
| statistics/ |