Resource
| Id | DNase-seq/ENCSR062DUU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR062DUU [biosample_summary="Homo sapiens stomach tissue female embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (105 days) output_type: peaks audit_warning: Replicate 1_2 has no significant footprints detected. audit_warning: Alignment file {ENCFF651VUW|/files/ENCFF651VUW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 34450254 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 {ENCFF651VUW|/files/ENCFF651VUW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.29. 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_ENCSR062DUU | float |
DNase-seq_ENCSR062DUU |
DNase-seq ENCSR062DUU [biosample_summary="Homo sapiens stomach tissue female embryo (105 days)"]
|
 |
[0.234, 20.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7608364 | 0.24% | 41985 |
| chr1 | 714105 | 0.29% | 3934 |
| chr2 | 602872 | 0.25% | 3369 |
| chr3 | 503056 | 0.25% | 2787 |
| chr4 | 372688 | 0.20% | 2070 |
| chr5 | 402482 | 0.22% | 2259 |
| chr6 | 463830 | 0.27% | 2548 |
| chr7 | 372676 | 0.23% | 2115 |
| chr8 | 333955 | 0.23% | 1879 |
| chr9 | 320877 | 0.23% | 1769 |
| chr10 | 350231 | 0.26% | 1969 |
| chr11 | 400784 | 0.30% | 2193 |
| chr12 | 385155 | 0.29% | 2122 |
| chr13 | 191089 | 0.17% | 1060 |
| chr14 | 242682 | 0.23% | 1329 |
| chr15 | 245852 | 0.24% | 1371 |
| chr16 | 261870 | 0.29% | 1406 |
| chr17 | 322530 | 0.39% | 1753 |
| chr18 | 153399 | 0.19% | 866 |
| chr19 | 361759 | 0.62% | 1832 |
| chr20 | 198861 | 0.31% | 1101 |
| chr21 | 81866 | 0.18% | 457 |
| chr22 | 128565 | 0.25% | 708 |
| chrX | 191107 | 0.12% | 1055 |
| chrY | 6073 | 0.01% | 33 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41985 | 3 | 920 | 181.22 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF935XVZ.bed.gz | 443.48 KB | 2ead62499cf226785bc3ff3f579b3b0a |
| ENCFF935XVZ.tabix.bed.gz | 394.04 KB | 717943b122799d74d1a275d9ab32c5f2 |
| ENCFF935XVZ.tabix.bed.gz.tbi | 252.17 KB | d26ab7fe3ecc2105d599e5924ffba61b |
| genomic_resource.yaml | 2.73 KB | 0a0eb5feee96d237ecfa359480cd1ea5 |
| statistics/ |