Resource
| Id | DNase-seq/ENCSR198JXW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR198JXW [biosample_summary="Homo sapiens muscle of leg tissue female embryo (85 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (85 days) output_type: peaks audit_warning: Alignment file {ENCFF691HJH|/files/ENCFF691HJH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 33611194 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 {ENCFF691HJH|/files/ENCFF691HJH/} 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_ENCSR198JXW | float |
DNase-seq_ENCSR198JXW |
DNase-seq ENCSR198JXW [biosample_summary="Homo sapiens muscle of leg tissue female embryo (85 days)"]
|
 |
[0.239, 11.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9065931 | 0.28% | 47904 |
| chr1 | 827720 | 0.33% | 4335 |
| chr2 | 709289 | 0.29% | 3818 |
| chr3 | 599226 | 0.30% | 3137 |
| chr4 | 466931 | 0.25% | 2501 |
| chr5 | 492664 | 0.27% | 2623 |
| chr6 | 554822 | 0.32% | 2906 |
| chr7 | 449499 | 0.28% | 2408 |
| chr8 | 417238 | 0.29% | 2223 |
| chr9 | 380119 | 0.27% | 2012 |
| chr10 | 428259 | 0.32% | 2279 |
| chr11 | 477722 | 0.35% | 2526 |
| chr12 | 472928 | 0.35% | 2469 |
| chr13 | 239248 | 0.21% | 1298 |
| chr14 | 302629 | 0.28% | 1568 |
| chr15 | 295691 | 0.29% | 1579 |
| chr16 | 272735 | 0.30% | 1422 |
| chr17 | 369873 | 0.44% | 1962 |
| chr18 | 192200 | 0.24% | 1039 |
| chr19 | 400947 | 0.68% | 1931 |
| chr20 | 224225 | 0.35% | 1212 |
| chr21 | 98065 | 0.21% | 527 |
| chr22 | 151522 | 0.30% | 809 |
| chrX | 242239 | 0.16% | 1319 |
| chrY | 140 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 47904 | 1 | 880 | 189.25 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF240TIB.bed.gz | 493.85 KB | 3869bea07e1431961a0dd039c4b4891c |
| ENCFF240TIB.tabix.bed.gz | 445.42 KB | 6660e94aea0a022cccc4d0a2a7d9efcd |
| ENCFF240TIB.tabix.bed.gz.tbi | 266.31 KB | d7f5c05cf6d37514e9f4d0b174ad86c8 |
| genomic_resource.yaml | 2.67 KB | f19e64523f9b5d9287b9e6f77180524a |
| statistics/ |