Resource
| Id | DNase-seq/ENCSR921PPJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR921PPJ [biosample_summary="Homo sapiens with mild cognitive impairment; dorsolateral prefrontal cortex tissue female adult (83 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (83 years) with mild cognitive impairment 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 {ENCFF054OWB|/files/ENCFF054OWB/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.35. 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_ENCSR921PPJ | float |
DNase-seq_ENCSR921PPJ |
DNase-seq ENCSR921PPJ [biosample_summary="Homo sapiens with mild cognitive impairment; dorsolateral prefrontal cortex tissue female adult (83 years)"]
|
 |
[0.0946, 19.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10437382 | 0.32% | 58176 |
| chr1 | 972272 | 0.39% | 5439 |
| chr2 | 796410 | 0.33% | 4499 |
| chr3 | 581843 | 0.29% | 3289 |
| chr4 | 388437 | 0.20% | 2168 |
| chr5 | 505142 | 0.28% | 2874 |
| chr6 | 520319 | 0.30% | 2913 |
| chr7 | 504585 | 0.32% | 2804 |
| chr8 | 453490 | 0.31% | 2552 |
| chr9 | 487218 | 0.35% | 2720 |
| chr10 | 520265 | 0.39% | 2919 |
| chr11 | 619575 | 0.46% | 3480 |
| chr12 | 481195 | 0.36% | 2661 |
| chr13 | 194455 | 0.17% | 1106 |
| chr14 | 338608 | 0.32% | 1883 |
| chr15 | 361075 | 0.35% | 2013 |
| chr16 | 410546 | 0.45% | 2234 |
| chr17 | 557566 | 0.67% | 3066 |
| chr18 | 193259 | 0.24% | 1101 |
| chr19 | 573062 | 0.98% | 2981 |
| chr20 | 317056 | 0.49% | 1774 |
| chr21 | 132565 | 0.28% | 742 |
| chr22 | 301212 | 0.59% | 1709 |
| chrX | 226836 | 0.15% | 1246 |
| chrY | 391 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 58176 | 3 | 820 | 179.41 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF752ZTJ.bed.gz | 640.96 KB | a015d25da6e78070b3bab21a363841e2 |
| ENCFF752ZTJ.tabix.bed.gz | 579.92 KB | 3bf6b5001143d8f25905dd2df297eae4 |
| ENCFF752ZTJ.tabix.bed.gz.tbi | 276.59 KB | 72756d67195a2a921e4da8a3ba47cd2b |
| genomic_resource.yaml | 2.26 KB | a538e45502c9025bf41a80688e0919bf |
| statistics/ |