Resource
| Id | DNase-seq/ENCSR712PYJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR712PYJ [biosample_summary="Homo sapiens ovary tissue female adult (30 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (30 years) output_type: peaks audit_internal_action: Archived analysis {ENCAN414TJN|/analyses/ENCAN414TJN/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF946WRC|/files/ENCFF946WRC/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 47591014 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 {ENCFF764PYL|/files/ENCFF764PYL/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 47193769 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 {ENCFF764PYL|/files/ENCFF764PYL/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.32. 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_ENCSR712PYJ | float |
DNase-seq_ENCSR712PYJ |
DNase-seq ENCSR712PYJ [biosample_summary="Homo sapiens ovary tissue female adult (30 years)"]
|
 |
[5, 1.01e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 13146237 | 0.41% | 87388 |
| chr1 | 1230958 | 0.49% | 8186 |
| chr2 | 1058338 | 0.44% | 7033 |
| chr3 | 888446 | 0.45% | 5905 |
| chr4 | 634616 | 0.33% | 4216 |
| chr5 | 709720 | 0.39% | 4716 |
| chr6 | 785207 | 0.46% | 5221 |
| chr7 | 645553 | 0.41% | 4290 |
| chr8 | 582460 | 0.40% | 3870 |
| chr9 | 560542 | 0.41% | 3727 |
| chr10 | 667614 | 0.50% | 4437 |
| chr11 | 669627 | 0.50% | 4450 |
| chr12 | 646271 | 0.48% | 4301 |
| chr13 | 318099 | 0.28% | 2116 |
| chr14 | 422644 | 0.39% | 2813 |
| chr15 | 436455 | 0.43% | 2899 |
| chr16 | 429737 | 0.48% | 2863 |
| chr17 | 559283 | 0.67% | 3718 |
| chr18 | 290392 | 0.36% | 1925 |
| chr19 | 469062 | 0.80% | 3123 |
| chr20 | 339434 | 0.53% | 2257 |
| chr21 | 148950 | 0.32% | 992 |
| chr22 | 245759 | 0.48% | 1631 |
| chrX | 406320 | 0.26% | 2694 |
| chrY | 750 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 87388 | 32 | 450 | 150.44 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF936ENC.bed.gz | 853.32 KB | 9e564cc5860cb209c81260040435c022 |
| ENCFF936ENC.tabix.bed.gz | 732.72 KB | d65bc8082f341710bb89bdd7216bc7d4 |
| ENCFF936ENC.tabix.bed.gz.tbi | 410.98 KB | 1176a6c834695715093f27cea325d2b8 |
| genomic_resource.yaml | 3.38 KB | 33078f39b4794ad508316eb0238019cf |
| statistics/ |