Resource
| Id | DNase-seq/ENCSR301RCD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR301RCD [biosample_summary="Homo sapiens renal pelvis tissue male embryo (127 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (127 days) output_type: peaks audit_warning: Alignment file {ENCFF646GPT|/files/ENCFF646GPT/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 30585813 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 {ENCFF646GPT|/files/ENCFF646GPT/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.30. 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_ENCSR301RCD | float |
DNase-seq_ENCSR301RCD |
DNase-seq ENCSR301RCD [biosample_summary="Homo sapiens renal pelvis tissue male embryo (127 days)"]
|
 |
[0.263, 21.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6362685 | 0.20% | 34251 |
| chr1 | 597224 | 0.24% | 3176 |
| chr2 | 507367 | 0.21% | 2759 |
| chr3 | 416891 | 0.21% | 2285 |
| chr4 | 311797 | 0.16% | 1700 |
| chr5 | 354238 | 0.20% | 1915 |
| chr6 | 380805 | 0.22% | 2051 |
| chr7 | 305847 | 0.19% | 1660 |
| chr8 | 269025 | 0.19% | 1490 |
| chr9 | 265935 | 0.19% | 1450 |
| chr10 | 299665 | 0.22% | 1637 |
| chr11 | 337015 | 0.25% | 1781 |
| chr12 | 313828 | 0.24% | 1696 |
| chr13 | 155086 | 0.14% | 854 |
| chr14 | 203201 | 0.19% | 1067 |
| chr15 | 204638 | 0.20% | 1127 |
| chr16 | 205112 | 0.23% | 1126 |
| chr17 | 261168 | 0.31% | 1364 |
| chr18 | 142053 | 0.18% | 771 |
| chr19 | 330482 | 0.56% | 1564 |
| chr20 | 168366 | 0.26% | 936 |
| chr21 | 71478 | 0.15% | 412 |
| chr22 | 107140 | 0.21% | 575 |
| chrX | 147550 | 0.09% | 819 |
| chrY | 6774 | 0.01% | 36 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 34251 | 2 | 920 | 185.77 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF073RBO.bed.gz | 356.79 KB | 31529a07fb623c70953f226b6e96183f |
| ENCFF073RBO.tabix.bed.gz | 318.96 KB | c1414318bd29d1b4e43812bf667077a4 |
| ENCFF073RBO.tabix.bed.gz.tbi | 208.63 KB | 08a053b9e060849d380595a5849d4229 |
| genomic_resource.yaml | 2.66 KB | 2f5de72da1f9f9a622f7dee2da367397 |
| statistics/ |