Resource
| Id | DNase-seq/ENCSR502NDK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR502NDK [biosample_summary="Homo sapiens small intestine tissue female embryo (108 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (108 days) output_type: peaks audit_warning: Alignment file {ENCFF645ZJZ|/files/ENCFF645ZJZ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 44834849 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 {ENCFF645ZJZ|/files/ENCFF645ZJZ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.30. 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_ENCSR502NDK | float |
DNase-seq_ENCSR502NDK |
DNase-seq ENCSR502NDK [biosample_summary="Homo sapiens small intestine tissue female embryo (108 days)"]
|
 |
[0.179, 15.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10619723 | 0.33% | 54940 |
| chr1 | 1018508 | 0.41% | 5263 |
| chr2 | 833954 | 0.34% | 4356 |
| chr3 | 696090 | 0.35% | 3641 |
| chr4 | 534623 | 0.28% | 2779 |
| chr5 | 540834 | 0.30% | 2863 |
| chr6 | 656907 | 0.38% | 3367 |
| chr7 | 559400 | 0.35% | 2908 |
| chr8 | 464896 | 0.32% | 2423 |
| chr9 | 442245 | 0.32% | 2288 |
| chr10 | 480497 | 0.36% | 2530 |
| chr11 | 546811 | 0.40% | 2854 |
| chr12 | 537860 | 0.40% | 2726 |
| chr13 | 262621 | 0.23% | 1361 |
| chr14 | 346940 | 0.32% | 1757 |
| chr15 | 341668 | 0.33% | 1771 |
| chr16 | 350451 | 0.39% | 1839 |
| chr17 | 460307 | 0.55% | 2360 |
| chr18 | 231798 | 0.29% | 1208 |
| chr19 | 453208 | 0.77% | 2167 |
| chr20 | 276154 | 0.43% | 1448 |
| chr21 | 116047 | 0.25% | 590 |
| chr22 | 186671 | 0.37% | 953 |
| chrX | 280844 | 0.18% | 1485 |
| chrY | 389 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 54940 | 1 | 800 | 193.3 | 193 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF107WTD.bed.gz | 579.94 KB | af14714e73ab92d1d12c1bc41cc0b166 |
| ENCFF107WTD.tabix.bed.gz | 519.79 KB | 9783f242e90d517a50583caae29db86e |
| ENCFF107WTD.tabix.bed.gz.tbi | 294.15 KB | d5328d2862171d02750866622c96c2d4 |
| genomic_resource.yaml | 2.68 KB | 2901db25e4e2baf86337c64cf0f49a38 |
| statistics/ |