Resource
| Id | DNase-seq/ENCSR428XAX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR428XAX [biosample_summary="Homo sapiens ovary tissue female embryo"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo output_type: peaks audit_warning: Alignment file {ENCFF803UUA|/files/ENCFF803UUA/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 30412138 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 {ENCFF803UUA|/files/ENCFF803UUA/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) 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-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR428XAX | float |
DNase-seq_ENCSR428XAX |
DNase-seq ENCSR428XAX [biosample_summary="Homo sapiens ovary tissue female embryo"]
|
 |
[0.231, 12.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8518675 | 0.26% | 42088 |
| chr1 | 808620 | 0.32% | 3986 |
| chr2 | 648419 | 0.27% | 3216 |
| chr3 | 536638 | 0.27% | 2626 |
| chr4 | 431594 | 0.23% | 2067 |
| chr5 | 451947 | 0.25% | 2215 |
| chr6 | 516024 | 0.30% | 2513 |
| chr7 | 440022 | 0.28% | 2154 |
| chr8 | 373761 | 0.26% | 1897 |
| chr9 | 360413 | 0.26% | 1777 |
| chr10 | 379207 | 0.28% | 1907 |
| chr11 | 429545 | 0.32% | 2129 |
| chr12 | 425902 | 0.32% | 2128 |
| chr13 | 207732 | 0.18% | 1010 |
| chr14 | 285294 | 0.27% | 1388 |
| chr15 | 283970 | 0.28% | 1415 |
| chr16 | 288597 | 0.32% | 1458 |
| chr17 | 357329 | 0.43% | 1795 |
| chr18 | 177491 | 0.22% | 890 |
| chr19 | 414477 | 0.71% | 1962 |
| chr20 | 205062 | 0.32% | 1083 |
| chr21 | 87184 | 0.19% | 447 |
| chr22 | 145539 | 0.29% | 754 |
| chrX | 263768 | 0.17% | 1270 |
| chrY | 140 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 42088 | 3 | 940 | 202.4 | 183 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF770ZGN.bed.gz | 431.91 KB | c711180b3008a6afa503f171b0c25ef9 |
| ENCFF770ZGN.tabix.bed.gz | 392.31 KB | 843b33383830d23c89bfa3466f2adcb4 |
| ENCFF770ZGN.tabix.bed.gz.tbi | 230.82 KB | 78f13fd4172e511d9c7cc39d5709ccf8 |
| genomic_resource.yaml | 2.59 KB | 5ccd7cef743012579e3a6d58a142d80e |
| statistics/ |