Resource
| Id | DNase-seq/ENCSR000EJI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EJI [biosample_summary="Homo sapiens GM18507"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: peaks audit_error: 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 {ENCFF804MVE|/files/ENCFF804MVE/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.24. 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/}) audit_internal_action: Released analysis {ENCAN750IRT|/analyses/ENCAN750IRT/} has in progress subobject document {0c03826d-e284-4042-9a14-70f8d870efc5|/documents/0c03826d-e284-4042-9a14-70f8d870efc5/} audit_warning: Alignment file {ENCFF804MVE|/files/ENCFF804MVE/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 39642445 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000EJI | float |
DNase-seq_ENCSR000EJI |
DNase-seq ENCSR000EJI [biosample_summary="Homo sapiens GM18507"]
|
 |
[0.232, 12.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6952781 | 0.22% | 39983 |
| chr1 | 696083 | 0.28% | 3978 |
| chr2 | 509875 | 0.21% | 2950 |
| chr3 | 414256 | 0.21% | 2415 |
| chr4 | 270458 | 0.14% | 1602 |
| chr5 | 337599 | 0.19% | 1985 |
| chr6 | 382694 | 0.22% | 2241 |
| chr7 | 343096 | 0.22% | 1981 |
| chr8 | 279117 | 0.19% | 1633 |
| chr9 | 291554 | 0.21% | 1663 |
| chr10 | 318725 | 0.24% | 1872 |
| chr11 | 376622 | 0.28% | 2171 |
| chr12 | 351054 | 0.26% | 2025 |
| chr13 | 148315 | 0.13% | 863 |
| chr14 | 234498 | 0.22% | 1327 |
| chr15 | 227047 | 0.22% | 1323 |
| chr16 | 283103 | 0.31% | 1599 |
| chr17 | 371862 | 0.45% | 2096 |
| chr18 | 128090 | 0.16% | 745 |
| chr19 | 404586 | 0.69% | 2143 |
| chr20 | 199825 | 0.31% | 1165 |
| chr21 | 73082 | 0.16% | 430 |
| chr22 | 160529 | 0.32% | 910 |
| chrX | 146307 | 0.09% | 842 |
| chrY | 4404 | 0.01% | 24 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 39983 | 2 | 820 | 173.89 | 174 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF587IIJ.bed.gz | 422.74 KB | 9c70e429bb289ac189270ff6f4b30aef |
| ENCFF587IIJ.tabix.bed.gz | 378.75 KB | 4c1309ac178dc6b4495a10eed1f0f95c |
| ENCFF587IIJ.tabix.bed.gz.tbi | 233.54 KB | fb8ef56444b7e9e00c92766f399ec15b |
| genomic_resource.yaml | 2.76 KB | fd5cac8541e44d20cf1d07c272f418f1 |
| statistics/ |