Resource
| Id | DNase-seq/ENCSR871APX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR871APX [biosample_summary="Homo sapiens right kidney tissue female embryo (147 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (147 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN328QEC|/analyses/ENCAN328QEC/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF289TZA|/files/ENCFF289TZA/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 37881644 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/}) audit_warning: Alignment file {ENCFF685FBO|/files/ENCFF685FBO/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 37587071 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/}) 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 {ENCFF685FBO|/files/ENCFF685FBO/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.36. 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR871APX | float |
DNase-seq_ENCSR871APX |
DNase-seq ENCSR871APX [biosample_summary="Homo sapiens right kidney tissue female embryo (147 days)"]
|
 |
[4, 755] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12650107 | 0.39% | 83990 |
| chr1 | 1128926 | 0.45% | 7498 |
| chr2 | 1031266 | 0.43% | 6844 |
| chr3 | 813030 | 0.41% | 5397 |
| chr4 | 692771 | 0.36% | 4590 |
| chr5 | 715171 | 0.39% | 4742 |
| chr6 | 770697 | 0.45% | 5116 |
| chr7 | 656600 | 0.41% | 4347 |
| chr8 | 590086 | 0.41% | 3925 |
| chr9 | 537570 | 0.39% | 3567 |
| chr10 | 608461 | 0.45% | 4051 |
| chr11 | 643871 | 0.48% | 4272 |
| chr12 | 632589 | 0.47% | 4203 |
| chr13 | 346437 | 0.30% | 2297 |
| chr14 | 406136 | 0.38% | 2693 |
| chr15 | 414434 | 0.41% | 2753 |
| chr16 | 397697 | 0.44% | 2639 |
| chr17 | 484568 | 0.58% | 3227 |
| chr18 | 305476 | 0.38% | 2031 |
| chr19 | 422746 | 0.72% | 2812 |
| chr20 | 316690 | 0.49% | 2105 |
| chr21 | 146042 | 0.31% | 973 |
| chr22 | 214631 | 0.42% | 1425 |
| chrX | 373612 | 0.24% | 2479 |
| chrY | 600 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 83990 | 10 | 450 | 150.61 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF929WJR.bed.gz | 813.8 KB | 6c21d0eaf087d7bc5e5d4a25cb4aa8e8 |
| ENCFF929WJR.tabix.bed.gz | 697.75 KB | 2d22461315dcb03c1ee16cad1a62e413 |
| ENCFF929WJR.tabix.bed.gz.tbi | 421.59 KB | b222343ea4dc0fe457c2f39607308623 |
| genomic_resource.yaml | 3.41 KB | bed9768cf5e87482d7facab85c7b4326 |
| statistics/ |