Resource
| Id | DNase-seq/ENCSR752NTF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR752NTF [biosample_summary="Homo sapiens right renal pelvis tissue male embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (105 days) output_type: peaks audit_warning: Alignment file {ENCFF250JPZ|/files/ENCFF250JPZ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 34146551 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 {ENCFF250JPZ|/files/ENCFF250JPZ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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_ENCSR752NTF | float |
DNase-seq_ENCSR752NTF |
DNase-seq ENCSR752NTF [biosample_summary="Homo sapiens right renal pelvis tissue male embryo (105 days)"]
|
 |
[0.235, 20.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9386954 | 0.29% | 46120 |
| chr1 | 887117 | 0.36% | 4342 |
| chr2 | 741267 | 0.31% | 3622 |
| chr3 | 603946 | 0.30% | 2937 |
| chr4 | 477146 | 0.25% | 2278 |
| chr5 | 509201 | 0.28% | 2529 |
| chr6 | 589772 | 0.35% | 2852 |
| chr7 | 474458 | 0.30% | 2349 |
| chr8 | 421900 | 0.29% | 2129 |
| chr9 | 392744 | 0.28% | 1949 |
| chr10 | 448873 | 0.34% | 2222 |
| chr11 | 476393 | 0.35% | 2322 |
| chr12 | 479279 | 0.36% | 2346 |
| chr13 | 228622 | 0.20% | 1144 |
| chr14 | 312476 | 0.29% | 1491 |
| chr15 | 312182 | 0.31% | 1547 |
| chr16 | 290130 | 0.32% | 1445 |
| chr17 | 391907 | 0.47% | 1931 |
| chr18 | 198657 | 0.25% | 996 |
| chr19 | 441221 | 0.75% | 2034 |
| chr20 | 221617 | 0.34% | 1164 |
| chr21 | 96989 | 0.21% | 481 |
| chr22 | 154869 | 0.30% | 794 |
| chrX | 226677 | 0.15% | 1172 |
| chrY | 9511 | 0.02% | 44 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 46120 | 1 | 1020 | 203.53 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF778TSG.bed.gz | 472.47 KB | 7d07cb23c9d708d6feb1ba3c05928964 |
| ENCFF778TSG.tabix.bed.gz | 432.08 KB | 4326b64de5cf62cbb03211c9c5d864ba |
| ENCFF778TSG.tabix.bed.gz.tbi | 243.27 KB | e38a3c8c4333fc6d25ae3bf59e9de654 |
| genomic_resource.yaml | 2.68 KB | 5669f026b6c0ff7c18070f5abc4ba782 |
| statistics/ |