Resource
| Id | DNase-seq/ENCSR274FZD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR274FZD [biosample_summary="Homo sapiens with Cognitive impairment, Alzheimer''s disease; 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 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 {ENCFF773CBJ|/files/ENCFF773CBJ/} processed by DNase-seq ENCODE4 v3.0.0 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_ENCSR274FZD | float |
DNase-seq_ENCSR274FZD |
DNase-seq ENCSR274FZD [biosample_summary="Homo sapiens with Cognitive impairment, Alzheimer''s disease; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.0676, 18.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11726149 | 0.36% | 64178 |
| chr1 | 1077944 | 0.43% | 5941 |
| chr2 | 938258 | 0.39% | 5196 |
| chr3 | 605096 | 0.31% | 3261 |
| chr4 | 431343 | 0.23% | 2325 |
| chr5 | 578004 | 0.32% | 3192 |
| chr6 | 587528 | 0.34% | 3174 |
| chr7 | 591553 | 0.37% | 3288 |
| chr8 | 475947 | 0.33% | 2614 |
| chr9 | 524086 | 0.38% | 2855 |
| chr10 | 612301 | 0.46% | 3375 |
| chr11 | 668050 | 0.49% | 3687 |
| chr12 | 523345 | 0.39% | 2821 |
| chr13 | 220261 | 0.19% | 1221 |
| chr14 | 371723 | 0.35% | 2023 |
| chr15 | 382527 | 0.38% | 2118 |
| chr16 | 471417 | 0.52% | 2564 |
| chr17 | 608324 | 0.73% | 3292 |
| chr18 | 231197 | 0.29% | 1304 |
| chr19 | 648848 | 1.11% | 3379 |
| chr20 | 362937 | 0.56% | 2028 |
| chr21 | 149383 | 0.32% | 841 |
| chr22 | 399100 | 0.79% | 2227 |
| chrX | 266168 | 0.17% | 1445 |
| chrY | 809 | <0.01% | 7 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 64178 | 2 | 940 | 182.71 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF601IBY.bed.gz | 700.37 KB | 60149ae6d2dc0fa2645cef26fc3c55dd |
| ENCFF601IBY.tabix.bed.gz | 635.3 KB | f8cc4e43fb0bf21b396078bd983baab4 |
| ENCFF601IBY.tabix.bed.gz.tbi | 259.85 KB | 7ae6bc7ba4053da033910139fdf85d14 |
| genomic_resource.yaml | 2.37 KB | da28ab4a40cfe3696bf11a25214a1915 |
| statistics/ |