Resource
| Id | DNase-seq/ENCSR475VQD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR475VQD [biosample_summary="Homo sapiens brain tissue male embryo (72 days) and male embryo (76 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (72 days) male embryo (76 days) output_type: peaks audit_warning: Alignment file {ENCFF878NAE|/files/ENCFF878NAE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 42397848 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 {ENCFF878NAE|/files/ENCFF878NAE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR475VQD | float |
DNase-seq_ENCSR475VQD |
DNase-seq ENCSR475VQD [biosample_summary="Homo sapiens brain tissue male embryo (72 days) and male embryo (76 days)"]
|
 |
[0.0266, 42.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 52952853 | 1.65% | 248244 |
| chr1 | 4523269 | 1.82% | 21012 |
| chr2 | 4454247 | 1.84% | 20853 |
| chr3 | 3524830 | 1.78% | 16619 |
| chr4 | 2938158 | 1.54% | 13940 |
| chr5 | 3189993 | 1.76% | 14941 |
| chr6 | 3202794 | 1.88% | 14919 |
| chr7 | 2839299 | 1.78% | 13192 |
| chr8 | 2626717 | 1.81% | 12342 |
| chr9 | 2220656 | 1.60% | 10442 |
| chr10 | 2616729 | 1.96% | 12240 |
| chr11 | 2633595 | 1.95% | 12327 |
| chr12 | 2504128 | 1.88% | 11832 |
| chr13 | 1680053 | 1.47% | 7871 |
| chr14 | 1718900 | 1.61% | 7967 |
| chr15 | 1647741 | 1.62% | 7702 |
| chr16 | 1739486 | 1.93% | 8068 |
| chr17 | 1897757 | 2.28% | 8845 |
| chr18 | 1393225 | 1.73% | 6530 |
| chr19 | 1253581 | 2.14% | 5892 |
| chr20 | 1364002 | 2.12% | 6396 |
| chr21 | 602470 | 1.29% | 2836 |
| chr22 | 850460 | 1.67% | 4009 |
| chrX | 1479434 | 0.95% | 7201 |
| chrY | 51329 | 0.09% | 268 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 248244 | 1 | 1200 | 213.31 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF224LZZ.bed.gz | 2.64 MB | 80e8cfdb09f17636c7b4e77572207e82 |
| ENCFF224LZZ.tabix.bed.gz | 2.42 MB | 72f4e39fae16ae391ba9276252a05892 |
| ENCFF224LZZ.tabix.bed.gz.tbi | 768.23 KB | 6f493dbe6f7ea1663a36b6d6307f781f |
| genomic_resource.yaml | 2.76 KB | 0fc708b75a6561125d94753450afdb5e |
| statistics/ |