Resource
| Id | DNase-seq/ENCSR148MFM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR148MFM [biosample_summary="Homo sapiens spinal cord tissue male embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (105 days) output_type: peaks audit_warning: Alignment file {ENCFF524MZP|/files/ENCFF524MZP/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 40694852 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 {ENCFF524MZP|/files/ENCFF524MZP/} 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_ENCSR148MFM | float |
DNase-seq_ENCSR148MFM |
DNase-seq ENCSR148MFM [biosample_summary="Homo sapiens spinal cord tissue male embryo (105 days)"]
|
 |
[0.172, 8.28] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7950036 | 0.25% | 37873 |
| chr1 | 730612 | 0.29% | 3455 |
| chr2 | 611343 | 0.25% | 2954 |
| chr3 | 576579 | 0.29% | 2671 |
| chr4 | 418941 | 0.22% | 1981 |
| chr5 | 474219 | 0.26% | 2219 |
| chr6 | 520537 | 0.30% | 2399 |
| chr7 | 401706 | 0.25% | 1965 |
| chr8 | 345134 | 0.24% | 1698 |
| chr9 | 323006 | 0.23% | 1577 |
| chr10 | 335877 | 0.25% | 1652 |
| chr11 | 398382 | 0.29% | 1889 |
| chr12 | 418800 | 0.31% | 1937 |
| chr13 | 197943 | 0.17% | 945 |
| chr14 | 266834 | 0.25% | 1237 |
| chr15 | 257434 | 0.25% | 1226 |
| chr16 | 239583 | 0.27% | 1180 |
| chr17 | 326576 | 0.39% | 1559 |
| chr18 | 178108 | 0.22% | 849 |
| chr19 | 344073 | 0.59% | 1548 |
| chr20 | 175395 | 0.27% | 886 |
| chr21 | 76641 | 0.16% | 378 |
| chr22 | 130104 | 0.26% | 656 |
| chrX | 194647 | 0.12% | 975 |
| chrY | 7562 | 0.01% | 37 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 37873 | 1 | 1052 | 209.91 | 193 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF087YEH.bed.gz | 381.77 KB | 1e436d32d2c1d652c588b970c258e199 |
| ENCFF087YEH.tabix.bed.gz | 352.72 KB | 3a4af3b54852d198ffd3430e8aff50af |
| ENCFF087YEH.tabix.bed.gz.tbi | 192.68 KB | 48f56c7361c1260c18e154f997172ecb |
| genomic_resource.yaml | 2.66 KB | cb668741d911dc2ed328edc062548945 |
| statistics/ |