Resource
| Id | DNase-seq/ENCSR670ZSA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR670ZSA [biosample_summary="Homo sapiens right 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 {ENCFF199PNS|/files/ENCFF199PNS/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 37458872 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 {ENCFF199PNS|/files/ENCFF199PNS/} 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_ENCSR670ZSA | float |
DNase-seq_ENCSR670ZSA |
DNase-seq ENCSR670ZSA [biosample_summary="Homo sapiens right kidney tissue male embryo (96 days)"]
|
 |
[0.214, 11.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8323254 | 0.26% | 40568 |
| chr1 | 770556 | 0.31% | 3683 |
| chr2 | 680788 | 0.28% | 3288 |
| chr3 | 558283 | 0.28% | 2730 |
| chr4 | 436634 | 0.23% | 2099 |
| chr5 | 481495 | 0.27% | 2324 |
| chr6 | 544201 | 0.32% | 2587 |
| chr7 | 411741 | 0.26% | 2007 |
| chr8 | 363368 | 0.25% | 1786 |
| chr9 | 331985 | 0.24% | 1664 |
| chr10 | 390512 | 0.29% | 1941 |
| chr11 | 426834 | 0.32% | 2081 |
| chr12 | 420510 | 0.32% | 2026 |
| chr13 | 212172 | 0.19% | 1019 |
| chr14 | 272784 | 0.25% | 1318 |
| chr15 | 278215 | 0.27% | 1377 |
| chr16 | 254941 | 0.28% | 1277 |
| chr17 | 314747 | 0.38% | 1564 |
| chr18 | 176382 | 0.22% | 891 |
| chr19 | 389513 | 0.66% | 1787 |
| chr20 | 198633 | 0.31% | 1024 |
| chr21 | 82082 | 0.18% | 412 |
| chr22 | 128987 | 0.25% | 672 |
| chrX | 188393 | 0.12% | 970 |
| chrY | 9498 | 0.02% | 41 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 40568 | 1 | 1160 | 205.17 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF748WYJ.bed.gz | 407.92 KB | 5318dcdf9b3ea2dd0e816634cee2f3ee |
| ENCFF748WYJ.tabix.bed.gz | 374.49 KB | f8021ad76c8f4b7cabca0a93a9698d12 |
| ENCFF748WYJ.tabix.bed.gz.tbi | 211.88 KB | 39e5502996273e6afb0afd3b30db9f21 |
| genomic_resource.yaml | 2.65 KB | 484f5f5fedd42cd3716aa3a1560c7c44 |
| statistics/ |