Resource
| Id | DNase-seq/ENCSR305UJX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR305UJX [biosample_summary="Homo sapiens heart tissue male child (3 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male child (3 years) output_type: peaks audit_warning: Alignment file {ENCFF867EBM|/files/ENCFF867EBM/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 36747000 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 {ENCFF867EBM|/files/ENCFF867EBM/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.31. 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_ENCSR305UJX | float |
DNase-seq_ENCSR305UJX |
DNase-seq ENCSR305UJX [biosample_summary="Homo sapiens heart tissue male child (3 years)"]
|
 |
[0.219, 11.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8958282 | 0.28% | 49075 |
| chr1 | 842133 | 0.34% | 4636 |
| chr2 | 706957 | 0.29% | 3913 |
| chr3 | 606552 | 0.31% | 3338 |
| chr4 | 425097 | 0.22% | 2349 |
| chr5 | 505342 | 0.28% | 2787 |
| chr6 | 536520 | 0.31% | 2961 |
| chr7 | 451836 | 0.28% | 2493 |
| chr8 | 398251 | 0.27% | 2213 |
| chr9 | 382821 | 0.28% | 2093 |
| chr10 | 425258 | 0.32% | 2367 |
| chr11 | 467704 | 0.35% | 2552 |
| chr12 | 458757 | 0.34% | 2501 |
| chr13 | 232872 | 0.20% | 1275 |
| chr14 | 275648 | 0.26% | 1485 |
| chr15 | 303521 | 0.30% | 1660 |
| chr16 | 288750 | 0.32% | 1583 |
| chr17 | 379109 | 0.46% | 2014 |
| chr18 | 193550 | 0.24% | 1082 |
| chr19 | 391043 | 0.67% | 1946 |
| chr20 | 222821 | 0.35% | 1255 |
| chr21 | 102815 | 0.22% | 564 |
| chr22 | 165132 | 0.32% | 901 |
| chrX | 185818 | 0.12% | 1045 |
| chrY | 9975 | 0.02% | 62 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 49075 | 3 | 780 | 182.54 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF730ORU.bed.gz | 518.12 KB | 09050cdc99615067e80f5bb071a69b3b |
| ENCFF730ORU.tabix.bed.gz | 460.84 KB | 93c94f4b4cb89704b07ccea020ccd348 |
| ENCFF730ORU.tabix.bed.gz.tbi | 289.46 KB | b45696bd4b8e244c8da69ab0f35dede0 |
| genomic_resource.yaml | 2.63 KB | 94f2b4adcaca9cd20154712c0bb12dd9 |
| statistics/ |