Resource
| Id | DNase-seq/ENCSR499IFY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR499IFY [biosample_summary="Homo sapiens placenta tissue embryo (53 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: embryo (53 days) output_type: peaks 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 {ENCFF025ERJ|/files/ENCFF025ERJ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.31. 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_ENCSR499IFY | float |
DNase-seq_ENCSR499IFY |
DNase-seq ENCSR499IFY [biosample_summary="Homo sapiens placenta tissue embryo (53 days)"]
|
 |
[0.024, 9.18] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 30411664 | 0.95% | 166816 |
| chr1 | 2998389 | 1.20% | 16362 |
| chr2 | 2323872 | 0.96% | 12884 |
| chr3 | 2021689 | 1.02% | 11082 |
| chr4 | 1494080 | 0.79% | 8309 |
| chr5 | 1628599 | 0.90% | 9047 |
| chr6 | 1935967 | 1.13% | 10570 |
| chr7 | 1589740 | 1.00% | 8800 |
| chr8 | 1284858 | 0.89% | 7081 |
| chr9 | 1314926 | 0.95% | 7170 |
| chr10 | 1348976 | 1.01% | 7412 |
| chr11 | 1518710 | 1.12% | 8281 |
| chr12 | 1572313 | 1.18% | 8519 |
| chr13 | 716229 | 0.63% | 3942 |
| chr14 | 978868 | 0.91% | 5343 |
| chr15 | 961932 | 0.94% | 5264 |
| chr16 | 965444 | 1.07% | 5286 |
| chr17 | 1317781 | 1.58% | 7195 |
| chr18 | 598081 | 0.74% | 3314 |
| chr19 | 1320280 | 2.25% | 7020 |
| chr20 | 746428 | 1.16% | 4064 |
| chr21 | 325292 | 0.70% | 1787 |
| chr22 | 589795 | 1.16% | 3228 |
| chrX | 805123 | 0.52% | 4530 |
| chrY | 54292 | 0.09% | 326 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 166816 | 1 | 900 | 182.31 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF491ZQT.bed.gz | 1.78 MB | aa1659f686129ae5cb8bc539663b3c28 |
| ENCFF491ZQT.tabix.bed.gz | 1.63 MB | bde3b7bee6f10a6a2c25d002fe16f2dc |
| ENCFF491ZQT.tabix.bed.gz.tbi | 519.51 KB | bf5c77d0e31f7d1bf3472b7fe1accca7 |
| genomic_resource.yaml | 2.0 KB | 30b8b631ffcebcb23b7ac74a928f4c20 |
| statistics/ |