Resource
| Id | DNase-seq/ENCSR984SDD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR984SDD [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (90 or above years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (90 or above 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 {ENCFF903EVF|/files/ENCFF903EVF/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.29. 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_ENCSR984SDD | float |
DNase-seq_ENCSR984SDD |
DNase-seq ENCSR984SDD [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.0733, 14.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11632269 | 0.36% | 64282 |
| chr1 | 1122021 | 0.45% | 6142 |
| chr2 | 842734 | 0.35% | 4737 |
| chr3 | 658355 | 0.33% | 3655 |
| chr4 | 443187 | 0.23% | 2467 |
| chr5 | 570212 | 0.31% | 3180 |
| chr6 | 611185 | 0.36% | 3376 |
| chr7 | 562237 | 0.35% | 3190 |
| chr8 | 490570 | 0.34% | 2759 |
| chr9 | 506338 | 0.37% | 2813 |
| chr10 | 567776 | 0.42% | 3184 |
| chr11 | 646566 | 0.48% | 3543 |
| chr12 | 561436 | 0.42% | 3049 |
| chr13 | 247676 | 0.22% | 1399 |
| chr14 | 375480 | 0.35% | 2052 |
| chr15 | 406404 | 0.40% | 2298 |
| chr16 | 477241 | 0.53% | 2613 |
| chr17 | 621317 | 0.75% | 3348 |
| chr18 | 206365 | 0.26% | 1193 |
| chr19 | 657125 | 1.12% | 3380 |
| chr20 | 360091 | 0.56% | 2024 |
| chr21 | 135908 | 0.29% | 759 |
| chr22 | 300676 | 0.59% | 1685 |
| chrX | 260900 | 0.17% | 1431 |
| chrY | 469 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 64282 | 1 | 740 | 180.96 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF333NJK.bed.gz | 710.2 KB | ab0c139616c2714b884ca0a63f8a5454 |
| ENCFF333NJK.tabix.bed.gz | 643.12 KB | 90581966ba3d503ecdc2bb98eb96bda8 |
| ENCFF333NJK.tabix.bed.gz.tbi | 306.55 KB | 3c342951fa1ccb895f172d1e5c87e8d5 |
| genomic_resource.yaml | 2.28 KB | 3dd255060a7e14026665e960ba02a922 |
| statistics/ |