Resource
| Id | DNase-seq/ENCSR612IKQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR612IKQ [biosample_summary="Homo sapiens with Cognitive impairment, Alzheimer''s disease; posterior cingulate gyrus tissue female adult (87 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female 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 {ENCFF176HYT|/files/ENCFF176HYT/} 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_ENCSR612IKQ | float |
DNase-seq_ENCSR612IKQ |
DNase-seq ENCSR612IKQ [biosample_summary="Homo sapiens with Cognitive impairment, Alzheimer''s disease; posterior cingulate gyrus tissue female adult (87 years)"]
|
 |
[0.0561, 15.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 14505754 | 0.45% | 80329 |
| chr1 | 1275806 | 0.51% | 7155 |
| chr2 | 1387688 | 0.57% | 7656 |
| chr3 | 758259 | 0.38% | 4184 |
| chr4 | 447391 | 0.24% | 2538 |
| chr5 | 695357 | 0.38% | 3835 |
| chr6 | 613712 | 0.36% | 3421 |
| chr7 | 775806 | 0.49% | 4337 |
| chr8 | 611734 | 0.42% | 3408 |
| chr9 | 637341 | 0.46% | 3559 |
| chr10 | 883814 | 0.66% | 4830 |
| chr11 | 816368 | 0.60% | 4492 |
| chr12 | 548827 | 0.41% | 3108 |
| chr13 | 298601 | 0.26% | 1679 |
| chr14 | 539055 | 0.50% | 2966 |
| chr15 | 545764 | 0.54% | 3070 |
| chr16 | 497995 | 0.55% | 2767 |
| chr17 | 773345 | 0.93% | 4272 |
| chr18 | 290960 | 0.36% | 1625 |
| chr19 | 604956 | 1.03% | 3230 |
| chr20 | 449845 | 0.70% | 2500 |
| chr21 | 231489 | 0.50% | 1254 |
| chr22 | 555033 | 1.09% | 2971 |
| chrX | 265764 | 0.17% | 1464 |
| chrY | 844 | <0.01% | 8 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 80329 | 2 | 1040 | 180.58 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF010XTH.bed.gz | 833.95 KB | 53114081e8e64f3a7edb89f737275b6a |
| ENCFF010XTH.tabix.bed.gz | 762.13 KB | e5213bc935319bc21bc4e4914d154f4f |
| ENCFF010XTH.tabix.bed.gz.tbi | 261.47 KB | 816a17406de24e8de21112e0bcb39962 |
| genomic_resource.yaml | 2.33 KB | 6d37c8f0beeeb58a7e55143fea51eaf3 |
| statistics/ |