Resource
| Id | DNase-seq/ENCSR062DXC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR062DXC [biosample_summary="Homo sapiens muscle of arm tissue female embryo (115 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (115 days) output_type: peaks audit_warning: Alignment file {ENCFF845KHW|/files/ENCFF845KHW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 23043593 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 {ENCFF845KHW|/files/ENCFF845KHW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.32. 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_ENCSR062DXC | float |
DNase-seq_ENCSR062DXC |
DNase-seq ENCSR062DXC [biosample_summary="Homo sapiens muscle of arm tissue female embryo (115 days)"]
|
 |
[0.305, 10.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5497332 | 0.17% | 29676 |
| chr1 | 523838 | 0.21% | 2801 |
| chr2 | 433575 | 0.18% | 2329 |
| chr3 | 362710 | 0.18% | 1965 |
| chr4 | 273870 | 0.14% | 1504 |
| chr5 | 288242 | 0.16% | 1573 |
| chr6 | 332365 | 0.19% | 1792 |
| chr7 | 266062 | 0.17% | 1453 |
| chr8 | 241294 | 0.17% | 1320 |
| chr9 | 226720 | 0.16% | 1227 |
| chr10 | 242236 | 0.18% | 1374 |
| chr11 | 292161 | 0.22% | 1569 |
| chr12 | 291353 | 0.22% | 1543 |
| chr13 | 135050 | 0.12% | 724 |
| chr14 | 189989 | 0.18% | 1009 |
| chr15 | 170301 | 0.17% | 935 |
| chr16 | 178810 | 0.20% | 983 |
| chr17 | 234458 | 0.28% | 1237 |
| chr18 | 111669 | 0.14% | 629 |
| chr19 | 274368 | 0.47% | 1350 |
| chr20 | 137421 | 0.21% | 762 |
| chr21 | 59414 | 0.13% | 336 |
| chr22 | 93861 | 0.18% | 499 |
| chrX | 137565 | 0.09% | 762 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 29676 | 2 | 860 | 185.25 | 174 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF349WKN.bed.gz | 305.09 KB | ebba05dd27f45c8261687609f7f00b15 |
| ENCFF349WKN.tabix.bed.gz | 272.43 KB | 3d832d3f3ef26a01782c2122d25552d4 |
| ENCFF349WKN.tabix.bed.gz.tbi | 184.97 KB | 939bdf9043e0736089d2dbeb5e1e2cf7 |
| genomic_resource.yaml | 2.67 KB | 0d2fcb3ad6cb735ec377465547fbc517 |
| statistics/ |