Resource
| Id | DNase-seq/ENCSR938UOR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR938UOR [biosample_summary="Homo sapiens muscle of leg tissue female embryo (115 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (115 days) output_type: peaks audit_warning: Alignment file {ENCFF956NIR|/files/ENCFF956NIR/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 20760260 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 {ENCFF956NIR|/files/ENCFF956NIR/} 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_ENCSR938UOR | float |
DNase-seq_ENCSR938UOR |
DNase-seq ENCSR938UOR [biosample_summary="Homo sapiens muscle of leg tissue female embryo (115 days)"]
|
 |
[0.387, 12.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4233084 | 0.13% | 22890 |
| chr1 | 399681 | 0.16% | 2125 |
| chr2 | 341856 | 0.14% | 1841 |
| chr3 | 278574 | 0.14% | 1500 |
| chr4 | 213304 | 0.11% | 1171 |
| chr5 | 232319 | 0.13% | 1253 |
| chr6 | 255065 | 0.15% | 1402 |
| chr7 | 198016 | 0.12% | 1090 |
| chr8 | 179243 | 0.12% | 991 |
| chr9 | 181272 | 0.13% | 977 |
| chr10 | 187036 | 0.14% | 1038 |
| chr11 | 216629 | 0.16% | 1183 |
| chr12 | 214067 | 0.16% | 1161 |
| chr13 | 111764 | 0.10% | 619 |
| chr14 | 129777 | 0.12% | 690 |
| chr15 | 131684 | 0.13% | 740 |
| chr16 | 137241 | 0.15% | 719 |
| chr17 | 181655 | 0.22% | 964 |
| chr18 | 82627 | 0.10% | 460 |
| chr19 | 220267 | 0.38% | 1076 |
| chr20 | 105844 | 0.16% | 570 |
| chr21 | 46638 | 0.10% | 261 |
| chr22 | 69856 | 0.14% | 391 |
| chrX | 118509 | 0.08% | 667 |
| chrY | 160 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 22890 | 1 | 860 | 184.93 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF055FYP.bed.gz | 236.65 KB | 31dab0062b1a721506104eaa6ae0ab26 |
| ENCFF055FYP.tabix.bed.gz | 210.88 KB | c0c69f3c9c05f9ca9ebe3a7fe8c726ad |
| ENCFF055FYP.tabix.bed.gz.tbi | 149.79 KB | f7f093930bed0cce745fcbd364de845f |
| genomic_resource.yaml | 2.67 KB | ce1773aa25b20aab5a14782c27595e39 |
| statistics/ |