Resource
| Id | DNase-seq/ENCSR000EMU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EMU [biosample_summary="Homo sapiens H1"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: peaks audit_internal_action: Archived analysis {ENCAN956AZA|/analyses/ENCAN956AZA/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF742AKX|/files/ENCFF742AKX/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 24393501 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/}) audit_warning: Alignment file {ENCFF546PJU|/files/ENCFF546PJU/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 24119556 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/}) 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 {ENCFF546PJU|/files/ENCFF546PJU/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000EMU | float |
DNase-seq_ENCSR000EMU |
DNase-seq ENCSR000EMU [biosample_summary="Homo sapiens H1"]
|
 |
[3, 1.41e+04] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9013812 | 0.28% | 59994 |
| chr1 | 846010 | 0.34% | 5634 |
| chr2 | 702597 | 0.29% | 4674 |
| chr3 | 573300 | 0.29% | 3814 |
| chr4 | 443250 | 0.23% | 2950 |
| chr5 | 489300 | 0.27% | 3257 |
| chr6 | 518478 | 0.30% | 3451 |
| chr7 | 470267 | 0.30% | 3130 |
| chr8 | 395211 | 0.27% | 2628 |
| chr9 | 373495 | 0.27% | 2488 |
| chr10 | 418930 | 0.31% | 2784 |
| chr11 | 468505 | 0.35% | 3116 |
| chr12 | 432587 | 0.32% | 2881 |
| chr13 | 230836 | 0.20% | 1535 |
| chr14 | 282078 | 0.26% | 1878 |
| chr15 | 278919 | 0.27% | 1857 |
| chr16 | 319650 | 0.35% | 2128 |
| chr17 | 374961 | 0.45% | 2498 |
| chr18 | 204750 | 0.25% | 1365 |
| chr19 | 406413 | 0.69% | 2709 |
| chr20 | 248550 | 0.39% | 1656 |
| chr21 | 95250 | 0.20% | 635 |
| chr22 | 164625 | 0.32% | 1094 |
| chrX | 262650 | 0.17% | 1745 |
| chrY | 13200 | 0.02% | 87 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 59994 | 43 | 300 | 150.25 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF030XPN.bed.gz | 583.29 KB | b0e8beca06f8f5ae796191b62e462988 |
| ENCFF030XPN.tabix.bed.gz | 501.76 KB | d81ef404ed67fb1a33d3a0f09aa5209d |
| ENCFF030XPN.tabix.bed.gz.tbi | 353.6 KB | 621b5d22df47e00da8257b06b3163cf6 |
| genomic_resource.yaml | 3.32 KB | 915fcd2c8673d65a31030444f4625199 |
| statistics/ |