Resource
| Id | DNase-seq/ENCSR608AHQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR608AHQ [biosample_summary="Homo sapiens stomach tissue male embryo (127 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (127 days) output_type: peaks audit_warning: Alignment file {ENCFF655BJW|/files/ENCFF655BJW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 30431116 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 {ENCFF655BJW|/files/ENCFF655BJW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR608AHQ | float |
DNase-seq_ENCSR608AHQ |
DNase-seq ENCSR608AHQ [biosample_summary="Homo sapiens stomach tissue male embryo (127 days)"]
|
 |
[0.231, 17.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7865506 | 0.24% | 40668 |
| chr1 | 738508 | 0.30% | 3799 |
| chr2 | 584351 | 0.24% | 3037 |
| chr3 | 505193 | 0.25% | 2581 |
| chr4 | 370251 | 0.19% | 1856 |
| chr5 | 405187 | 0.22% | 2081 |
| chr6 | 486435 | 0.28% | 2489 |
| chr7 | 389071 | 0.24% | 2060 |
| chr8 | 333316 | 0.23% | 1744 |
| chr9 | 339550 | 0.25% | 1765 |
| chr10 | 364736 | 0.27% | 1916 |
| chr11 | 390418 | 0.29% | 2044 |
| chr12 | 397146 | 0.30% | 2072 |
| chr13 | 189940 | 0.17% | 985 |
| chr14 | 262385 | 0.25% | 1333 |
| chr15 | 272704 | 0.27% | 1404 |
| chr16 | 277065 | 0.31% | 1443 |
| chr17 | 367990 | 0.44% | 1938 |
| chr18 | 155945 | 0.19% | 825 |
| chr19 | 406775 | 0.69% | 1980 |
| chr20 | 206091 | 0.32% | 1082 |
| chr21 | 83754 | 0.18% | 437 |
| chr22 | 141537 | 0.28% | 761 |
| chrX | 190615 | 0.12% | 999 |
| chrY | 6543 | 0.01% | 37 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 40668 | 1 | 940 | 193.41 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF894SPL.bed.gz | 421.73 KB | 9412d71b3d212df81e35c330f8443b98 |
| ENCFF894SPL.tabix.bed.gz | 382.55 KB | ad7469d20166f78ee545cf2076be5c1d |
| ENCFF894SPL.tabix.bed.gz.tbi | 226.11 KB | 3a95a6e7f1a4468d8f8e12a64709470c |
| genomic_resource.yaml | 2.64 KB | 2a091924622f899a3e2037b5e18272cf |
| statistics/ |