Resource
| Id | DNase-seq/ENCSR627KFV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR627KFV [biosample_summary="Homo sapiens stomach tissue female embryo (110 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (110 days) output_type: peaks audit_warning: Alignment file {ENCFF895DTV|/files/ENCFF895DTV/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 28929175 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 {ENCFF895DTV|/files/ENCFF895DTV/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.33. 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_ENCSR627KFV | float |
DNase-seq_ENCSR627KFV |
DNase-seq ENCSR627KFV [biosample_summary="Homo sapiens stomach tissue female embryo (110 days)"]
|
 |
[0.208, 10.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7253403 | 0.23% | 35791 |
| chr1 | 673790 | 0.27% | 3280 |
| chr2 | 561569 | 0.23% | 2777 |
| chr3 | 474463 | 0.24% | 2291 |
| chr4 | 364407 | 0.19% | 1753 |
| chr5 | 383472 | 0.21% | 1889 |
| chr6 | 471647 | 0.28% | 2287 |
| chr7 | 364625 | 0.23% | 1797 |
| chr8 | 302721 | 0.21% | 1535 |
| chr9 | 293618 | 0.21% | 1478 |
| chr10 | 327716 | 0.24% | 1638 |
| chr11 | 370599 | 0.27% | 1823 |
| chr12 | 374335 | 0.28% | 1839 |
| chr13 | 172980 | 0.15% | 860 |
| chr14 | 254689 | 0.24% | 1216 |
| chr15 | 242580 | 0.24% | 1229 |
| chr16 | 237370 | 0.26% | 1211 |
| chr17 | 315559 | 0.38% | 1575 |
| chr18 | 144310 | 0.18% | 743 |
| chr19 | 373160 | 0.64% | 1742 |
| chr20 | 173103 | 0.27% | 902 |
| chr21 | 75879 | 0.16% | 377 |
| chr22 | 115471 | 0.23% | 601 |
| chrX | 185118 | 0.12% | 946 |
| chrY | 222 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 35791 | 2 | 1080 | 202.66 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF012IZP.bed.gz | 362.34 KB | bb8370085d0e9bf398f43609f89d1970 |
| ENCFF012IZP.tabix.bed.gz | 332.68 KB | bbd33c8b3da0428261f3dff515074f38 |
| ENCFF012IZP.tabix.bed.gz.tbi | 190.68 KB | 74ad3322b5ee5bbc50073d571941b735 |
| genomic_resource.yaml | 2.65 KB | d0cc3f55f6d0793724c600a02eb7c9cb |
| statistics/ |