Resource
| Id | DNase-seq/ENCSR011VHK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR011VHK [biosample_summary="Homo sapiens with multiple sclerosis; naive B cell"] |
| Description |
status: released biological_replicates: Rep 1 summary: with multiple sclerosis output_type: peaks 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 {ENCFF528VKG|/files/ENCFF528VKG/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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_ENCSR011VHK | float |
DNase-seq_ENCSR011VHK |
DNase-seq ENCSR011VHK [biosample_summary="Homo sapiens with multiple sclerosis; naive B cell"]
|
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[0.13, 35.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12931653 | 0.40% | 62708 |
| chr1 | 1259195 | 0.51% | 6092 |
| chr2 | 945452 | 0.39% | 4584 |
| chr3 | 747341 | 0.38% | 3640 |
| chr4 | 508421 | 0.27% | 2456 |
| chr5 | 632754 | 0.35% | 3030 |
| chr6 | 840687 | 0.49% | 4029 |
| chr7 | 629740 | 0.40% | 3080 |
| chr8 | 528516 | 0.36% | 2598 |
| chr9 | 532883 | 0.39% | 2616 |
| chr10 | 570399 | 0.43% | 2754 |
| chr11 | 643225 | 0.48% | 3107 |
| chr12 | 686122 | 0.51% | 3308 |
| chr13 | 267154 | 0.23% | 1292 |
| chr14 | 439125 | 0.41% | 2143 |
| chr15 | 397254 | 0.39% | 1943 |
| chr16 | 481360 | 0.53% | 2370 |
| chr17 | 699773 | 0.84% | 3355 |
| chr18 | 238417 | 0.30% | 1179 |
| chr19 | 713162 | 1.22% | 3341 |
| chr20 | 322301 | 0.50% | 1627 |
| chr21 | 153795 | 0.33% | 744 |
| chr22 | 295891 | 0.58% | 1486 |
| chrX | 398268 | 0.26% | 1931 |
| chrY | 418 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 62708 | 3 | 940 | 206.22 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF581DQN.bed.gz | 688.76 KB | 9af037f654477f005e0f3a671a1dedaf |
| ENCFF581DQN.tabix.bed.gz | 633.4 KB | 1ebbd0d934f4323ed03120fbaa24e976 |
| ENCFF581DQN.tabix.bed.gz.tbi | 281.81 KB | 4aa6b2b5e2cf7beae7d3531472a2de5d |
| genomic_resource.yaml | 2.02 KB | a7013b513cf147aa86f7dcde444c24df |
| statistics/ |
