Resource
| Id | DNase-seq/ENCSR184DFF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR184DFF [biosample_summary="Homo sapiens left kidney tissue male embryo (96 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (96 days) output_type: peaks audit_warning: Alignment file {ENCFF231WEG|/files/ENCFF231WEG/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 34907340 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 {ENCFF231WEG|/files/ENCFF231WEG/} 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_ENCSR184DFF | float |
DNase-seq_ENCSR184DFF |
DNase-seq ENCSR184DFF [biosample_summary="Homo sapiens left kidney tissue male embryo (96 days)"]
|
 |
[0.23, 10.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8408890 | 0.26% | 40610 |
| chr1 | 790877 | 0.32% | 3684 |
| chr2 | 684332 | 0.28% | 3342 |
| chr3 | 570668 | 0.29% | 2680 |
| chr4 | 438224 | 0.23% | 2077 |
| chr5 | 464577 | 0.26% | 2219 |
| chr6 | 538401 | 0.32% | 2565 |
| chr7 | 420951 | 0.26% | 2081 |
| chr8 | 359750 | 0.25% | 1783 |
| chr9 | 326844 | 0.24% | 1609 |
| chr10 | 405790 | 0.30% | 1952 |
| chr11 | 422597 | 0.31% | 2052 |
| chr12 | 445612 | 0.33% | 2161 |
| chr13 | 210878 | 0.18% | 1023 |
| chr14 | 282574 | 0.26% | 1327 |
| chr15 | 287756 | 0.28% | 1377 |
| chr16 | 265570 | 0.29% | 1326 |
| chr17 | 336885 | 0.40% | 1679 |
| chr18 | 178600 | 0.22% | 873 |
| chr19 | 389380 | 0.66% | 1789 |
| chr20 | 189040 | 0.29% | 1005 |
| chr21 | 82786 | 0.18% | 416 |
| chr22 | 130191 | 0.26% | 650 |
| chrX | 176669 | 0.11% | 901 |
| chrY | 9938 | 0.02% | 39 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 40610 | 1 | 1180 | 207.06 | 184 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF615JYB.bed.gz | 406.55 KB | 04a75fb9a3ce9c5de4bd81dc0b8dd67c |
| ENCFF615JYB.tabix.bed.gz | 375.56 KB | 5390fc5b4ed8f6fb6c4e117a3601f71b |
| ENCFF615JYB.tabix.bed.gz.tbi | 204.88 KB | 407481be7252f831aa8aeeb0225bab59 |
| genomic_resource.yaml | 2.65 KB | e63b1d754ee4b70b4f12d78053b2a76d |
| statistics/ |