Resource
| Id | DNase-seq/ENCSR619DRM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR619DRM [biosample_summary="Homo sapiens renal pelvis tissue female embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (105 days) output_type: peaks audit_warning: Alignment file {ENCFF312ZAH|/files/ENCFF312ZAH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 21451378 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 {ENCFF312ZAH|/files/ENCFF312ZAH/} 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_ENCSR619DRM | float |
DNase-seq_ENCSR619DRM |
DNase-seq ENCSR619DRM [biosample_summary="Homo sapiens renal pelvis tissue female embryo (105 days)"]
|
 |
[0.328, 15.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5974910 | 0.19% | 33680 |
| chr1 | 578985 | 0.23% | 3257 |
| chr2 | 457717 | 0.19% | 2582 |
| chr3 | 370814 | 0.19% | 2089 |
| chr4 | 262070 | 0.14% | 1494 |
| chr5 | 303379 | 0.17% | 1738 |
| chr6 | 340041 | 0.20% | 1946 |
| chr7 | 284673 | 0.18% | 1659 |
| chr8 | 252122 | 0.17% | 1444 |
| chr9 | 250379 | 0.18% | 1402 |
| chr10 | 269398 | 0.20% | 1557 |
| chr11 | 318565 | 0.24% | 1767 |
| chr12 | 305834 | 0.23% | 1695 |
| chr13 | 128590 | 0.11% | 728 |
| chr14 | 196794 | 0.18% | 1084 |
| chr15 | 193471 | 0.19% | 1119 |
| chr16 | 214480 | 0.24% | 1203 |
| chr17 | 287813 | 0.35% | 1615 |
| chr18 | 117195 | 0.15% | 680 |
| chr19 | 342224 | 0.58% | 1774 |
| chr20 | 163002 | 0.25% | 944 |
| chr21 | 61960 | 0.13% | 352 |
| chr22 | 119018 | 0.23% | 681 |
| chrX | 156164 | 0.10% | 868 |
| chrY | 222 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 33680 | 2 | 780 | 177.4 | 173.5 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF156THP.bed.gz | 351.56 KB | 38484fb9fb4b80b4d7f3e7e7dca8158f |
| ENCFF156THP.tabix.bed.gz | 313.11 KB | 1603fbf1a43bcfbdbee9249afe3c4b54 |
| ENCFF156THP.tabix.bed.gz.tbi | 206.62 KB | 4720a1597ed9c6c63e888b0ecf363a72 |
| genomic_resource.yaml | 2.67 KB | 4ac38fe60d6b1c906f21910d27e89d51 |
| statistics/ |