Resource
| Id | DNase-seq/ENCSR860NDZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR860NDZ [biosample_summary="Homo sapiens small intestine tissue female embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (105 days) output_type: peaks audit_warning: Alignment file {ENCFF764WEH|/files/ENCFF764WEH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 39579658 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 {ENCFF764WEH|/files/ENCFF764WEH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) 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-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR860NDZ | float |
DNase-seq_ENCSR860NDZ |
DNase-seq ENCSR860NDZ [biosample_summary="Homo sapiens small intestine tissue female embryo (105 days)"]
|
 |
[0.203, 16.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12453025 | 0.39% | 67544 |
| chr1 | 1174935 | 0.47% | 6343 |
| chr2 | 1008836 | 0.42% | 5511 |
| chr3 | 834562 | 0.42% | 4584 |
| chr4 | 669389 | 0.35% | 3647 |
| chr5 | 682459 | 0.38% | 3698 |
| chr6 | 791020 | 0.46% | 4273 |
| chr7 | 640912 | 0.40% | 3482 |
| chr8 | 558968 | 0.39% | 3002 |
| chr9 | 513178 | 0.37% | 2803 |
| chr10 | 569466 | 0.43% | 3104 |
| chr11 | 655422 | 0.49% | 3554 |
| chr12 | 627245 | 0.47% | 3383 |
| chr13 | 333682 | 0.29% | 1821 |
| chr14 | 405522 | 0.38% | 2198 |
| chr15 | 381191 | 0.37% | 2082 |
| chr16 | 394432 | 0.44% | 2174 |
| chr17 | 492729 | 0.59% | 2655 |
| chr18 | 284895 | 0.35% | 1572 |
| chr19 | 452636 | 0.77% | 2286 |
| chr20 | 307159 | 0.48% | 1669 |
| chr21 | 135225 | 0.29% | 734 |
| chr22 | 208036 | 0.41% | 1127 |
| chrX | 330846 | 0.21% | 1840 |
| chrY | 280 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 67544 | 3 | 840 | 184.37 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF642RJM.bed.gz | 718.25 KB | 1b31fbcf0174b0398e650ec1d6a55f3b |
| ENCFF642RJM.tabix.bed.gz | 639.7 KB | 3f1688f64cf1d25e388465552efdc3dc |
| ENCFF642RJM.tabix.bed.gz.tbi | 355.75 KB | 5039a780da1ed5f7a525d878fb5806f4 |
| genomic_resource.yaml | 2.68 KB | 1e5d231e1ff2f0b09aa9f560fa8a81e3 |
| statistics/ |