Resource
| Id | DNase-seq/ENCSR511GQA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR511GQA [biosample_summary="Homo sapiens stomach tissue female embryo (108 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (108 days) output_type: peaks audit_error: Alignment file {ENCFF222ICK|/files/ENCFF222ICK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 19745618 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 {ENCFF222ICK|/files/ENCFF222ICK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.32. 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_ENCSR511GQA | float |
DNase-seq_ENCSR511GQA |
DNase-seq ENCSR511GQA [biosample_summary="Homo sapiens stomach tissue female embryo (108 days)"]
|
 |
[0.407, 20.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5272261 | 0.16% | 32369 |
| chr1 | 492925 | 0.20% | 3016 |
| chr2 | 415423 | 0.17% | 2582 |
| chr3 | 351244 | 0.18% | 2161 |
| chr4 | 269350 | 0.14% | 1683 |
| chr5 | 282759 | 0.16% | 1760 |
| chr6 | 309582 | 0.18% | 1915 |
| chr7 | 270502 | 0.17% | 1675 |
| chr8 | 237006 | 0.16% | 1488 |
| chr9 | 214625 | 0.16% | 1355 |
| chr10 | 244042 | 0.18% | 1528 |
| chr11 | 272330 | 0.20% | 1667 |
| chr12 | 270345 | 0.20% | 1639 |
| chr13 | 136341 | 0.12% | 849 |
| chr14 | 169931 | 0.16% | 1024 |
| chr15 | 166224 | 0.16% | 1010 |
| chr16 | 173588 | 0.19% | 1044 |
| chr17 | 220118 | 0.26% | 1325 |
| chr18 | 108691 | 0.14% | 690 |
| chr19 | 246367 | 0.42% | 1357 |
| chr20 | 133299 | 0.21% | 819 |
| chr21 | 56216 | 0.12% | 361 |
| chr22 | 84302 | 0.17% | 521 |
| chrX | 146891 | 0.09% | 899 |
| chrY | 160 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 32369 | 8 | 640 | 162.88 | 160 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF066YJZ.bed.gz | 336.31 KB | dabbfd15d7143cbbc40b3d4bea2e20a2 |
| ENCFF066YJZ.tabix.bed.gz | 296.28 KB | 7c6fa33d40fb159e2c7eaa713cd48b99 |
| ENCFF066YJZ.tabix.bed.gz.tbi | 225.11 KB | fe59d2c74fbebfe4b0717e5473f022ae |
| genomic_resource.yaml | 2.65 KB | 8f8bcc833a45a3b7942649034559a7b5 |
| statistics/ |