Resource
| Id | DNase-seq/ENCSR615WIN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR615WIN [biosample_summary="Homo sapiens spinal cord tissue female embryo (89 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (89 days) output_type: peaks audit_warning: Alignment file {ENCFF762XYC|/files/ENCFF762XYC/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 38335077 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 {ENCFF762XYC|/files/ENCFF762XYC/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) 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-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR615WIN | float |
DNase-seq_ENCSR615WIN |
DNase-seq ENCSR615WIN [biosample_summary="Homo sapiens spinal cord tissue female embryo (89 days)"]
|
 |
[0.183, 15.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11503906 | 0.36% | 61097 |
| chr1 | 1030876 | 0.41% | 5422 |
| chr2 | 880231 | 0.36% | 4708 |
| chr3 | 748025 | 0.38% | 4003 |
| chr4 | 592367 | 0.31% | 3146 |
| chr5 | 655046 | 0.36% | 3476 |
| chr6 | 707048 | 0.41% | 3695 |
| chr7 | 619256 | 0.39% | 3281 |
| chr8 | 530991 | 0.37% | 2851 |
| chr9 | 485643 | 0.35% | 2585 |
| chr10 | 523881 | 0.39% | 2801 |
| chr11 | 568832 | 0.42% | 3036 |
| chr12 | 560436 | 0.42% | 3004 |
| chr13 | 311314 | 0.27% | 1665 |
| chr14 | 380776 | 0.36% | 2001 |
| chr15 | 368765 | 0.36% | 1957 |
| chr16 | 385725 | 0.43% | 2052 |
| chr17 | 482612 | 0.58% | 2550 |
| chr18 | 255467 | 0.32% | 1388 |
| chr19 | 466138 | 0.80% | 2320 |
| chr20 | 285626 | 0.44% | 1560 |
| chr21 | 126370 | 0.27% | 678 |
| chr22 | 195676 | 0.39% | 1069 |
| chrX | 342665 | 0.22% | 1848 |
| chrY | 140 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 61097 | 1 | 870 | 188.29 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF473UNU.bed.gz | 644.08 KB | 231a44daa61a5cd7277d13f84051438e |
| ENCFF473UNU.tabix.bed.gz | 578.92 KB | b891f7795b168e1fb5f2c0fa36e7008e |
| ENCFF473UNU.tabix.bed.gz.tbi | 327.59 KB | b0595ef20fd84ab9dab30d72bda1084a |
| genomic_resource.yaml | 2.66 KB | f105ef300a764dfed941c1dfd6fe7ea6 |
| statistics/ |