Resource
| Id | DNase-seq/ENCSR726YMS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR726YMS [biosample_summary="Homo sapiens stomach tissue female embryo"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo output_type: peaks audit_internal_action: Archived analysis {ENCAN496DUS|/analyses/ENCAN496DUS/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF958QZF|/files/ENCFF958QZF/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 33599301 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 {ENCFF430FMO|/files/ENCFF430FMO/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 33352159 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 {ENCFF430FMO|/files/ENCFF430FMO/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR726YMS | float |
DNase-seq_ENCSR726YMS |
DNase-seq ENCSR726YMS [biosample_summary="Homo sapiens stomach tissue female embryo"]
|
 |
[4, 1.7e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12737177 | 0.40% | 84591 |
| chr1 | 1153934 | 0.46% | 7666 |
| chr2 | 1011431 | 0.42% | 6718 |
| chr3 | 826196 | 0.42% | 5483 |
| chr4 | 677050 | 0.36% | 4489 |
| chr5 | 693106 | 0.38% | 4598 |
| chr6 | 803152 | 0.47% | 5336 |
| chr7 | 656962 | 0.41% | 4363 |
| chr8 | 601831 | 0.41% | 3992 |
| chr9 | 524672 | 0.38% | 3489 |
| chr10 | 613936 | 0.46% | 4077 |
| chr11 | 649737 | 0.48% | 4321 |
| chr12 | 623815 | 0.47% | 4142 |
| chr13 | 346945 | 0.30% | 2305 |
| chr14 | 409016 | 0.38% | 2714 |
| chr15 | 408303 | 0.40% | 2713 |
| chr16 | 407106 | 0.45% | 2704 |
| chr17 | 518214 | 0.62% | 3447 |
| chr18 | 291880 | 0.36% | 1939 |
| chr19 | 468890 | 0.80% | 3118 |
| chr20 | 324516 | 0.50% | 2156 |
| chr21 | 146328 | 0.31% | 974 |
| chr22 | 221397 | 0.44% | 1465 |
| chrX | 342432 | 0.22% | 2273 |
| chrY | 16328 | 0.03% | 109 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 84591 | 13 | 600 | 150.57 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF716YVE.bed.gz | 821.85 KB | fa26e46e42a63d1d97ba929eb95a6af5 |
| ENCFF716YVE.tabix.bed.gz | 703.79 KB | 1ea9710f1cd472fdb00dab9946009c8d |
| ENCFF716YVE.tabix.bed.gz.tbi | 424.96 KB | 82e18d2de96ef0f3ccf85366dce8a7fe |
| genomic_resource.yaml | 3.34 KB | 619010e7ac8a66b1d1943051f162c114 |
| statistics/ |