Resource
| Id | DNase-seq/ENCSR512CWR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR512CWR [biosample_summary="Homo sapiens umbilical cord tissue embryo (59 days) and male embryo (76 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: embryo (59 days) male embryo (76 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 {ENCFF504SRC|/files/ENCFF504SRC/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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_ENCSR512CWR | float |
DNase-seq_ENCSR512CWR |
DNase-seq ENCSR512CWR [biosample_summary="Homo sapiens umbilical cord tissue embryo (59 days) and male embryo (76 days)"]
|
 |
[0.0284, 16.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 51260820 | 1.59% | 233073 |
| chr1 | 4577054 | 1.84% | 20646 |
| chr2 | 4257850 | 1.76% | 19412 |
| chr3 | 3466236 | 1.75% | 15628 |
| chr4 | 2888221 | 1.52% | 13106 |
| chr5 | 3107546 | 1.71% | 14078 |
| chr6 | 3154412 | 1.85% | 14244 |
| chr7 | 2647406 | 1.66% | 12050 |
| chr8 | 2450651 | 1.69% | 11084 |
| chr9 | 2212479 | 1.60% | 10076 |
| chr10 | 2614973 | 1.95% | 11807 |
| chr11 | 2640433 | 1.95% | 12026 |
| chr12 | 2550240 | 1.91% | 11546 |
| chr13 | 1546975 | 1.35% | 7033 |
| chr14 | 1570925 | 1.47% | 7148 |
| chr15 | 1603502 | 1.57% | 7339 |
| chr16 | 1508152 | 1.67% | 6852 |
| chr17 | 1908765 | 2.29% | 8726 |
| chr18 | 1186438 | 1.48% | 5428 |
| chr19 | 1228374 | 2.10% | 5575 |
| chr20 | 1211796 | 1.88% | 5575 |
| chr21 | 635937 | 1.36% | 2885 |
| chr22 | 774438 | 1.52% | 3628 |
| chrX | 1429462 | 0.92% | 6761 |
| chrY | 88555 | 0.15% | 420 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 233073 | 1 | 980 | 219.93 | 220 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF716MEI.bed.gz | 2.47 MB | 1d8945b348a4df3e3ebe89ae1f7df889 |
| ENCFF716MEI.tabix.bed.gz | 2.27 MB | 34f3fbb8744905177bf150a84e91612f |
| ENCFF716MEI.tabix.bed.gz.tbi | 704.1 KB | 1442b78c2f7395a7d908ed70f0bc139c |
| genomic_resource.yaml | 2.14 KB | 8718ef43f8fc36608b20648b88df2cbb |
| statistics/ |