Resource
| Id | DNase-seq/ENCSR782SSS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR782SSS [biosample_summary="Homo sapiens stomach tissue male adult (34 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: peaks audit_error: 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 {ENCFF974EMU|/files/ENCFF974EMU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.24. 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/}) audit_internal_action: Released analysis {ENCAN555AEW|/analyses/ENCAN555AEW/} has in progress subobject document {a6ea0a08-11e4-490b-97bd-475093df9aa7|/documents/a6ea0a08-11e4-490b-97bd-475093df9aa7/} audit_warning: Replicate 1_2 has no significant footprints detected. audit_warning: Alignment file {ENCFF974EMU|/files/ENCFF974EMU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 41097854 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR782SSS | float |
DNase-seq_ENCSR782SSS |
DNase-seq ENCSR782SSS [biosample_summary="Homo sapiens stomach tissue male adult (34 years)"]
|
 |
[0.196, 14.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10157023 | 0.32% | 57579 |
| chr1 | 957220 | 0.38% | 5465 |
| chr2 | 822569 | 0.34% | 4680 |
| chr3 | 689895 | 0.35% | 3881 |
| chr4 | 531710 | 0.28% | 3069 |
| chr5 | 544845 | 0.30% | 3118 |
| chr6 | 626224 | 0.37% | 3536 |
| chr7 | 515706 | 0.32% | 2906 |
| chr8 | 458452 | 0.32% | 2633 |
| chr9 | 442538 | 0.32% | 2482 |
| chr10 | 471783 | 0.35% | 2717 |
| chr11 | 506256 | 0.37% | 2897 |
| chr12 | 497325 | 0.37% | 2835 |
| chr13 | 259277 | 0.23% | 1476 |
| chr14 | 332663 | 0.31% | 1882 |
| chr15 | 322477 | 0.32% | 1832 |
| chr16 | 332409 | 0.37% | 1868 |
| chr17 | 439724 | 0.53% | 2463 |
| chr18 | 226399 | 0.28% | 1274 |
| chr19 | 376830 | 0.64% | 1956 |
| chr20 | 260725 | 0.40% | 1495 |
| chr21 | 112512 | 0.24% | 638 |
| chr22 | 170207 | 0.33% | 975 |
| chrX | 246354 | 0.16% | 1424 |
| chrY | 12923 | 0.02% | 77 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 57579 | 12 | 620 | 176.4 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF033LEB.bed.gz | 607.17 KB | 2b635f165939f652fc4b7d88515e0318 |
| ENCFF033LEB.tabix.bed.gz | 540.64 KB | 40c9c83e6a678afbaacb45bc3e05b1b6 |
| ENCFF033LEB.tabix.bed.gz.tbi | 321.44 KB | 47be7e520ef6c5defbe02a6666b397ad |
| genomic_resource.yaml | 2.93 KB | e3efa170b66dde1d771397bed52cfb26 |
| statistics/ |