Resource
| Id | DNase-seq/ENCSR000EJU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EJU [biosample_summary="Homo sapiens hepatocyte"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: peaks audit_internal_action: Released analysis {ENCAN161DFM|/analyses/ENCAN161DFM/} has in progress subobject document {2bd0f338-3b61-4111-81b9-d73beb3927bc|/documents/2bd0f338-3b61-4111-81b9-d73beb3927bc/} 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 {ENCFF345EXO|/files/ENCFF345EXO/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR000EJU | float |
DNase-seq_ENCSR000EJU |
DNase-seq ENCSR000EJU [biosample_summary="Homo sapiens hepatocyte"]
|
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[0.0859, 13.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4687458 | 0.15% | 29073 |
| chr1 | 430629 | 0.17% | 2713 |
| chr2 | 358301 | 0.15% | 2174 |
| chr3 | 245365 | 0.12% | 1550 |
| chr4 | 218152 | 0.11% | 1311 |
| chr5 | 209245 | 0.12% | 1322 |
| chr6 | 242745 | 0.14% | 1524 |
| chr7 | 247448 | 0.16% | 1512 |
| chr8 | 206484 | 0.14% | 1248 |
| chr9 | 211481 | 0.15% | 1312 |
| chr10 | 212237 | 0.16% | 1341 |
| chr11 | 279438 | 0.21% | 1734 |
| chr12 | 211487 | 0.16% | 1321 |
| chr13 | 98418 | 0.09% | 611 |
| chr14 | 143720 | 0.13% | 881 |
| chr15 | 138181 | 0.14% | 895 |
| chr16 | 203136 | 0.22% | 1241 |
| chr17 | 271550 | 0.33% | 1676 |
| chr18 | 86840 | 0.11% | 557 |
| chr19 | 323390 | 0.55% | 1908 |
| chr20 | 120737 | 0.19% | 753 |
| chr21 | 44897 | 0.10% | 298 |
| chr22 | 119296 | 0.23% | 760 |
| chrX | 64281 | 0.04% | 431 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 29073 | 3 | 1260 | 161.23 | 158 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF089ZNM.bed.gz | 310.31 KB | 495289e49eac87c42ad3809b24fd25ce |
| ENCFF089ZNM.tabix.bed.gz | 281.13 KB | 82091278b228856f6f2678f220d2e952 |
| ENCFF089ZNM.tabix.bed.gz.tbi | 135.29 KB | a9b4ec0b9c30733e8d4cf38beff6bc0f |
| genomic_resource.yaml | 2.14 KB | cb18f3978530bc321ee0630841ec94f7 |
| statistics/ |
