Resource
| Id | DNase-seq/ENCSR499PZA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR499PZA [biosample_summary="Homo sapiens kidney tissue male embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (105 days) output_type: peaks audit_warning: Alignment file {ENCFF813DOG|/files/ENCFF813DOG/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 28043677 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 {ENCFF813DOG|/files/ENCFF813DOG/} 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_ENCSR499PZA | float |
DNase-seq_ENCSR499PZA |
DNase-seq ENCSR499PZA [biosample_summary="Homo sapiens kidney tissue male embryo (105 days)"]
|
 |
[0.346, 85.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4814284 | 0.15% | 28069 |
| chr1 | 478917 | 0.19% | 2731 |
| chr2 | 363736 | 0.15% | 2171 |
| chr3 | 317557 | 0.16% | 1843 |
| chr4 | 221075 | 0.12% | 1344 |
| chr5 | 257915 | 0.14% | 1542 |
| chr6 | 283738 | 0.17% | 1682 |
| chr7 | 237975 | 0.15% | 1419 |
| chr8 | 200007 | 0.14% | 1196 |
| chr9 | 194233 | 0.14% | 1141 |
| chr10 | 209104 | 0.16% | 1242 |
| chr11 | 250226 | 0.19% | 1460 |
| chr12 | 241297 | 0.18% | 1373 |
| chr13 | 111022 | 0.10% | 654 |
| chr14 | 157849 | 0.15% | 910 |
| chr15 | 152342 | 0.15% | 871 |
| chr16 | 168228 | 0.19% | 963 |
| chr17 | 211332 | 0.25% | 1201 |
| chr18 | 87668 | 0.11% | 542 |
| chr19 | 286691 | 0.49% | 1475 |
| chr20 | 125618 | 0.19% | 754 |
| chr21 | 49207 | 0.11% | 294 |
| chr22 | 86004 | 0.17% | 508 |
| chrX | 118892 | 0.08% | 725 |
| chrY | 3651 | 0.01% | 28 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 28069 | 3 | 780 | 171.52 | 160 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF302YHA.bed.gz | 295.37 KB | a2d003506d1b91aa493b15fa2b9f8c69 |
| ENCFF302YHA.tabix.bed.gz | 264.01 KB | e4ca41c8bd62935df5c02c50f9ec6909 |
| ENCFF302YHA.tabix.bed.gz.tbi | 176.17 KB | c5143fb94f97cc450d4053a04afb1178 |
| genomic_resource.yaml | 2.64 KB | b4385e08396830318c45c044155c6ab4 |
| statistics/ |