Resource
| Id | DNase-seq/ENCSR076YBB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR076YBB [biosample_summary="Homo sapiens lung tissue male embryo (108 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (108 days) output_type: peaks audit_warning: Alignment file {ENCFF148XUS|/files/ENCFF148XUS/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 21577453 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 {ENCFF148XUS|/files/ENCFF148XUS/} 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_ENCSR076YBB | float |
DNase-seq_ENCSR076YBB |
DNase-seq ENCSR076YBB [biosample_summary="Homo sapiens lung tissue male embryo (108 days)"]
|
 |
[0.325, 15.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6961071 | 0.22% | 39802 |
| chr1 | 647543 | 0.26% | 3633 |
| chr2 | 544323 | 0.22% | 3142 |
| chr3 | 462864 | 0.23% | 2658 |
| chr4 | 351376 | 0.18% | 2025 |
| chr5 | 390801 | 0.22% | 2255 |
| chr6 | 427435 | 0.25% | 2397 |
| chr7 | 360965 | 0.23% | 2077 |
| chr8 | 323170 | 0.22% | 1895 |
| chr9 | 279795 | 0.20% | 1635 |
| chr10 | 331696 | 0.25% | 1918 |
| chr11 | 355380 | 0.26% | 2034 |
| chr12 | 362918 | 0.27% | 2046 |
| chr13 | 181026 | 0.16% | 1036 |
| chr14 | 220345 | 0.21% | 1243 |
| chr15 | 225255 | 0.22% | 1293 |
| chr16 | 215379 | 0.24% | 1236 |
| chr17 | 280535 | 0.34% | 1590 |
| chr18 | 147914 | 0.18% | 856 |
| chr19 | 296077 | 0.51% | 1566 |
| chr20 | 176485 | 0.27% | 1044 |
| chr21 | 75491 | 0.16% | 437 |
| chr22 | 114977 | 0.23% | 674 |
| chrX | 189181 | 0.12% | 1111 |
| chrY | 140 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 39802 | 2 | 780 | 174.89 | 160 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF778XBV.bed.gz | 417.25 KB | 63193a955bd443adc5af2c36a9745df0 |
| ENCFF778XBV.tabix.bed.gz | 368.4 KB | 1230af2ceab3e72d2ed0312cb55f12a8 |
| ENCFF778XBV.tabix.bed.gz.tbi | 255.83 KB | 2cf954b7a6ce37c26489a576dbf12146 |
| genomic_resource.yaml | 2.64 KB | 352e1de7e7d5821a71bed4c4ea7100a7 |
| statistics/ |