Resource
| Id | DNase-seq/ENCSR800QGE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR800QGE [biosample_summary="Homo sapiens large intestine tissue female embryo (103 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (103 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN288PDQ|/analyses/ENCAN288PDQ/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF049BTE|/files/ENCFF049BTE/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 25839859 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 {ENCFF562RWI|/files/ENCFF562RWI/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 25630989 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 {ENCFF562RWI|/files/ENCFF562RWI/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR800QGE | float |
DNase-seq_ENCSR800QGE |
DNase-seq ENCSR800QGE [biosample_summary="Homo sapiens large intestine tissue female embryo (103 days)"]
|
 |
[4, 814] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8083253 | 0.25% | 53628 |
| chr1 | 766631 | 0.31% | 5099 |
| chr2 | 647467 | 0.27% | 4290 |
| chr3 | 516772 | 0.26% | 3433 |
| chr4 | 405646 | 0.21% | 2694 |
| chr5 | 414984 | 0.23% | 2750 |
| chr6 | 495648 | 0.29% | 3291 |
| chr7 | 422782 | 0.27% | 2806 |
| chr8 | 360810 | 0.25% | 2394 |
| chr9 | 340310 | 0.25% | 2258 |
| chr10 | 376604 | 0.28% | 2502 |
| chr11 | 410693 | 0.30% | 2714 |
| chr12 | 402592 | 0.30% | 2664 |
| chr13 | 200555 | 0.18% | 1330 |
| chr14 | 263969 | 0.25% | 1750 |
| chr15 | 264996 | 0.26% | 1756 |
| chr16 | 273915 | 0.30% | 1819 |
| chr17 | 350644 | 0.42% | 2332 |
| chr18 | 175159 | 0.22% | 1159 |
| chr19 | 330976 | 0.56% | 2198 |
| chr20 | 203414 | 0.32% | 1352 |
| chr21 | 89100 | 0.19% | 590 |
| chr22 | 150809 | 0.30% | 999 |
| chrX | 218327 | 0.14% | 1445 |
| chrY | 450 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 53628 | 45 | 424 | 150.73 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF277ILM.bed.gz | 523.0 KB | 2b6429868df7450d4a5f4b985176c532 |
| ENCFF277ILM.tabix.bed.gz | 446.57 KB | ee8da8c2368d608385d4d2b2abbef546 |
| ENCFF277ILM.tabix.bed.gz.tbi | 296.51 KB | ea21b14876488141274c9d4118a0f068 |
| genomic_resource.yaml | 3.41 KB | 574dbd5f6783eadf81977c83a2faf1fb |
| statistics/ |