Resource
| Id | DNase-seq/ENCSR354FBA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR354FBA [biosample_summary="Homo sapiens small intestine tissue male embryo (115 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (115 days) output_type: peaks audit_error: Alignment file {ENCFF525BED|/files/ENCFF525BED/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 19441139 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 {ENCFF525BED|/files/ENCFF525BED/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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_ENCSR354FBA | float |
DNase-seq_ENCSR354FBA |
DNase-seq ENCSR354FBA [biosample_summary="Homo sapiens small intestine tissue male embryo (115 days)"]
|
 |
[0.361, 16.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6968430 | 0.22% | 40492 |
| chr1 | 677550 | 0.27% | 3891 |
| chr2 | 525647 | 0.22% | 3124 |
| chr3 | 435840 | 0.22% | 2594 |
| chr4 | 328822 | 0.17% | 1908 |
| chr5 | 350268 | 0.19% | 2072 |
| chr6 | 395753 | 0.23% | 2319 |
| chr7 | 353479 | 0.22% | 2065 |
| chr8 | 298400 | 0.21% | 1742 |
| chr9 | 292846 | 0.21% | 1721 |
| chr10 | 306056 | 0.23% | 1814 |
| chr11 | 367926 | 0.27% | 2147 |
| chr12 | 365306 | 0.27% | 2117 |
| chr13 | 162943 | 0.14% | 935 |
| chr14 | 228982 | 0.21% | 1305 |
| chr15 | 226009 | 0.22% | 1323 |
| chr16 | 248793 | 0.28% | 1423 |
| chr17 | 325442 | 0.39% | 1854 |
| chr18 | 149531 | 0.19% | 880 |
| chr19 | 365655 | 0.62% | 1942 |
| chr20 | 185236 | 0.29% | 1109 |
| chr21 | 78321 | 0.17% | 451 |
| chr22 | 139577 | 0.27% | 807 |
| chrX | 156401 | 0.10% | 929 |
| chrY | 3647 | 0.01% | 20 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 40492 | 7 | 760 | 172.09 | 160 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF835PEV.bed.gz | 425.8 KB | 47b00030e124f75deefbfcf8d76644fc |
| ENCFF835PEV.tabix.bed.gz | 376.34 KB | 82f451bf8282845b64c5b68825963fde |
| ENCFF835PEV.tabix.bed.gz.tbi | 250.21 KB | c3dbb94a6fdee38849fda327b0956ee8 |
| genomic_resource.yaml | 2.67 KB | 7736b2640e5d99b446c488aee81eadbd |
| statistics/ |