Resource
| Id | DNase-seq/ENCSR678ILN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR678ILN [biosample_summary="Homo sapiens ELF-1"] |
| Description |
status: released biological_replicates: Rep 2 summary: output_type: peaks audit_warning: Alignment file {ENCFF432EWQ|/files/ENCFF432EWQ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 31475418 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 {ENCFF432EWQ|/files/ENCFF432EWQ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.33. 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_ENCSR678ILN | float |
DNase-seq_ENCSR678ILN |
DNase-seq ENCSR678ILN [biosample_summary="Homo sapiens ELF-1"]
|
 |
[0.0314, 39.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 44002588 | 1.37% | 196587 |
| chr1 | 4047711 | 1.63% | 17795 |
| chr2 | 3429577 | 1.42% | 15491 |
| chr3 | 2586146 | 1.30% | 11707 |
| chr4 | 1937698 | 1.02% | 8774 |
| chr5 | 2345075 | 1.29% | 10588 |
| chr6 | 2510200 | 1.47% | 11178 |
| chr7 | 2246460 | 1.41% | 10053 |
| chr8 | 1981918 | 1.37% | 8936 |
| chr9 | 1782676 | 1.29% | 8046 |
| chr10 | 2107583 | 1.58% | 9455 |
| chr11 | 2296450 | 1.70% | 10192 |
| chr12 | 2096731 | 1.57% | 9400 |
| chr13 | 1095541 | 0.96% | 4952 |
| chr14 | 1350537 | 1.26% | 5989 |
| chr15 | 1415131 | 1.39% | 6312 |
| chr16 | 1560798 | 1.73% | 6919 |
| chr17 | 2041180 | 2.45% | 8907 |
| chr18 | 981250 | 1.22% | 4443 |
| chr19 | 1665609 | 2.84% | 7289 |
| chr20 | 1234512 | 1.92% | 5465 |
| chr21 | 477580 | 1.02% | 2136 |
| chr22 | 875520 | 1.72% | 3926 |
| chrX | 1935232 | 1.24% | 8624 |
| chrY | 1473 | <0.01% | 10 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 196587 | 1 | 1180 | 223.83 | 223 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF212CJT.bed.gz | 2.09 MB | 74c9f51793109bf080da601548d501e3 |
| ENCFF212CJT.tabix.bed.gz | 1.93 MB | 62120a493321f4b4e86730c34a524a49 |
| ENCFF212CJT.tabix.bed.gz.tbi | 624.19 KB | edddc60c8a614f4890864b50e62c8d3d |
| genomic_resource.yaml | 2.55 KB | e035f196b86dbe46c712b97ba4e34298 |
| statistics/ |