Resource
| Id | DNase-seq/ENCSR246PXX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR246PXX [biosample_summary="Homo sapiens stomach tissue male child (3 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male child (3 years) output_type: peaks audit_warning: Alignment file {ENCFF525YME|/files/ENCFF525YME/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 44440112 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 {ENCFF525YME|/files/ENCFF525YME/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.28. 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_ENCSR246PXX | float |
DNase-seq_ENCSR246PXX |
DNase-seq ENCSR246PXX [biosample_summary="Homo sapiens stomach tissue male child (3 years)"]
|
 |
[0.158, 14.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10229286 | 0.32% | 56929 |
| chr1 | 997678 | 0.40% | 5507 |
| chr2 | 804339 | 0.33% | 4548 |
| chr3 | 679099 | 0.34% | 3767 |
| chr4 | 512581 | 0.27% | 2914 |
| chr5 | 527590 | 0.29% | 2960 |
| chr6 | 625455 | 0.37% | 3495 |
| chr7 | 521380 | 0.33% | 2920 |
| chr8 | 449071 | 0.31% | 2502 |
| chr9 | 441850 | 0.32% | 2447 |
| chr10 | 456213 | 0.34% | 2610 |
| chr11 | 511807 | 0.38% | 2871 |
| chr12 | 506571 | 0.38% | 2813 |
| chr13 | 258005 | 0.23% | 1430 |
| chr14 | 336569 | 0.31% | 1878 |
| chr15 | 344565 | 0.34% | 1900 |
| chr16 | 338546 | 0.37% | 1866 |
| chr17 | 459310 | 0.55% | 2502 |
| chr18 | 217583 | 0.27% | 1226 |
| chr19 | 416095 | 0.71% | 2161 |
| chr20 | 268750 | 0.42% | 1487 |
| chr21 | 120394 | 0.26% | 681 |
| chr22 | 187132 | 0.37% | 1040 |
| chrX | 234925 | 0.15% | 1323 |
| chrY | 13778 | 0.02% | 81 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 56929 | 1 | 753 | 179.68 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF981ICF.bed.gz | 602.63 KB | 33dee29a47611b6b7b92c1e6bfac642a |
| ENCFF981ICF.tabix.bed.gz | 538.23 KB | 7bca2685cfe2d591d2d89f56e8536905 |
| ENCFF981ICF.tabix.bed.gz.tbi | 311.32 KB | 5d00839d7574399275ae448f1da8becd |
| genomic_resource.yaml | 2.63 KB | ec517ac828099d9656c23bd6970934cc |
| statistics/ |