Resource
| Id | DNase-seq/ENCSR097BWW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR097BWW [biosample_summary="Homo sapiens left kidney tissue female embryo (59 days) and male embryo (91 days)"] |
| Description |
status: released biological_replicates: Rep 2 summary: female embryo (59 days) male embryo (91 days) output_type: peaks audit_warning: Alignment file {ENCFF644KLS|/files/ENCFF644KLS/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 30845622 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 {ENCFF644KLS|/files/ENCFF644KLS/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.36. 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_ENCSR097BWW | float |
DNase-seq_ENCSR097BWW |
DNase-seq ENCSR097BWW [biosample_summary="Homo sapiens left kidney tissue female embryo (59 days) and male embryo (91 days)"]
|
 |
[0.0176, 28.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 57133445 | 1.78% | 280324 |
| chr1 | 5041777 | 2.03% | 24459 |
| chr2 | 4687632 | 1.94% | 23001 |
| chr3 | 3501747 | 1.77% | 17351 |
| chr4 | 2848706 | 1.50% | 14295 |
| chr5 | 3107586 | 1.71% | 15446 |
| chr6 | 3315351 | 1.94% | 16202 |
| chr7 | 2963225 | 1.86% | 14626 |
| chr8 | 2649275 | 1.83% | 13130 |
| chr9 | 2443000 | 1.77% | 12003 |
| chr10 | 2959463 | 2.21% | 14513 |
| chr11 | 2936955 | 2.17% | 14336 |
| chr12 | 2727962 | 2.05% | 13370 |
| chr13 | 1598186 | 1.40% | 7948 |
| chr14 | 1812542 | 1.69% | 8850 |
| chr15 | 1871500 | 1.83% | 9149 |
| chr16 | 1959351 | 2.17% | 9517 |
| chr17 | 2477462 | 2.98% | 11791 |
| chr18 | 1414879 | 1.76% | 6997 |
| chr19 | 1838010 | 3.14% | 8726 |
| chr20 | 1580495 | 2.45% | 7752 |
| chr21 | 665040 | 1.42% | 3268 |
| chr22 | 1076954 | 2.12% | 5272 |
| chrX | 1597675 | 1.02% | 8014 |
| chrY | 58672 | 0.10% | 308 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 280324 | 1 | 960 | 203.81 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF058HYK.bed.gz | 3.01 MB | f6f572c85d321b9836cae28d7f607714 |
| ENCFF058HYK.tabix.bed.gz | 2.75 MB | 10c0829ce1ed05f9deb3e1feb7c64690 |
| ENCFF058HYK.tabix.bed.gz.tbi | 751.65 KB | a143e4691d59880825602ac1c16b186c |
| genomic_resource.yaml | 2.78 KB | 5a7ba7a02f7cb9c3afc68811f5377939 |
| statistics/ |