Resource
| Id | DNase-seq/ENCSR839RAJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR839RAJ [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (85 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (85 years) with Alzheimer's disease 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 {ENCFF615RWO|/files/ENCFF615RWO/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 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_ENCSR839RAJ | float |
DNase-seq_ENCSR839RAJ |
DNase-seq ENCSR839RAJ [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (85 years)"]
|
 |
[0.0974, 15.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7661387 | 0.24% | 41276 |
| chr1 | 730627 | 0.29% | 3928 |
| chr2 | 586726 | 0.24% | 3212 |
| chr3 | 402978 | 0.20% | 2158 |
| chr4 | 288133 | 0.15% | 1567 |
| chr5 | 344647 | 0.19% | 1862 |
| chr6 | 365407 | 0.21% | 1979 |
| chr7 | 374902 | 0.24% | 2036 |
| chr8 | 329808 | 0.23% | 1779 |
| chr9 | 362024 | 0.26% | 1936 |
| chr10 | 382316 | 0.29% | 2087 |
| chr11 | 464970 | 0.34% | 2513 |
| chr12 | 349760 | 0.26% | 1859 |
| chr13 | 137075 | 0.12% | 732 |
| chr14 | 246884 | 0.23% | 1333 |
| chr15 | 242310 | 0.24% | 1299 |
| chr16 | 294942 | 0.33% | 1554 |
| chr17 | 427876 | 0.51% | 2299 |
| chr18 | 113916 | 0.14% | 630 |
| chr19 | 472582 | 0.81% | 2433 |
| chr20 | 218480 | 0.34% | 1229 |
| chr21 | 106671 | 0.23% | 612 |
| chr22 | 246555 | 0.49% | 1337 |
| chrX | 171562 | 0.11% | 900 |
| chrY | 236 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41276 | 3 | 760 | 185.61 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF994UFI.bed.gz | 455.89 KB | 91a752b033d99c204bab3c64a69b1ed3 |
| ENCFF994UFI.tabix.bed.gz | 412.19 KB | ccddf19cc812c96780d9afebde91901a |
| ENCFF994UFI.tabix.bed.gz.tbi | 200.33 KB | 997e43e572c6e8f2f43f4dad0e50bc2f |
| genomic_resource.yaml | 2.23 KB | cfa44261db52816979068b7ef122e874 |
| statistics/ |