Resource
| Id | DNase-seq/ENCSR904LMG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR904LMG [biosample_summary="Homo sapiens with Cognitive impairment, Alzheimer''s disease; dorsolateral prefrontal cortex tissue male adult (87 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (87 years) with Cognitive impairment, 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 {ENCFF855CLY|/files/ENCFF855CLY/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.28. 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_ENCSR904LMG | float |
DNase-seq_ENCSR904LMG |
DNase-seq ENCSR904LMG [biosample_summary="Homo sapiens with Cognitive impairment, Alzheimer''s disease; dorsolateral prefrontal cortex tissue male adult (87 years)"]
|
 |
[0.0582, 10.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12192944 | 0.38% | 66639 |
| chr1 | 1074964 | 0.43% | 5884 |
| chr2 | 1033401 | 0.43% | 5640 |
| chr3 | 614516 | 0.31% | 3406 |
| chr4 | 439398 | 0.23% | 2367 |
| chr5 | 623825 | 0.34% | 3448 |
| chr6 | 546963 | 0.32% | 3028 |
| chr7 | 629730 | 0.40% | 3427 |
| chr8 | 581078 | 0.40% | 3150 |
| chr9 | 542245 | 0.39% | 2979 |
| chr10 | 649886 | 0.49% | 3578 |
| chr11 | 694028 | 0.51% | 3750 |
| chr12 | 539242 | 0.40% | 2919 |
| chr13 | 278607 | 0.24% | 1513 |
| chr14 | 404238 | 0.38% | 2182 |
| chr15 | 419796 | 0.41% | 2308 |
| chr16 | 442036 | 0.49% | 2422 |
| chr17 | 577600 | 0.69% | 3194 |
| chr18 | 287619 | 0.36% | 1593 |
| chr19 | 594063 | 1.01% | 3113 |
| chr20 | 377786 | 0.59% | 2154 |
| chr21 | 172178 | 0.37% | 954 |
| chr22 | 427763 | 0.84% | 2299 |
| chrX | 232934 | 0.15% | 1277 |
| chrY | 9048 | 0.02% | 54 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 66639 | 2 | 860 | 182.97 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF577DIL.bed.gz | 704.84 KB | 2b426ac1da8d0cf13cc16ed5c0b27f9f |
| ENCFF577DIL.tabix.bed.gz | 646.37 KB | c96421652125dd2b509dc9a59a954ae7 |
| ENCFF577DIL.tabix.bed.gz.tbi | 245.57 KB | e7459e38db6f944e9937b1a8abaf9950 |
| genomic_resource.yaml | 2.34 KB | b11b88208918d2c0190cf2b7edfb2dbe |
| statistics/ |