Resource
| Id | DNase-seq/ENCSR730IHD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR730IHD [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (90 or above years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (90 or above years) with 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 {ENCFF513GGQ|/files/ENCFF513GGQ/} 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_ENCSR730IHD | float |
DNase-seq_ENCSR730IHD |
DNase-seq ENCSR730IHD [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (90 or above years)"]
|
 |
[0.118, 10.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5452587 | 0.17% | 30103 |
| chr1 | 547213 | 0.22% | 3005 |
| chr2 | 441341 | 0.18% | 2487 |
| chr3 | 272755 | 0.14% | 1489 |
| chr4 | 194927 | 0.10% | 1056 |
| chr5 | 248425 | 0.14% | 1399 |
| chr6 | 254091 | 0.15% | 1418 |
| chr7 | 245583 | 0.15% | 1355 |
| chr8 | 231928 | 0.16% | 1304 |
| chr9 | 238617 | 0.17% | 1333 |
| chr10 | 254713 | 0.19% | 1466 |
| chr11 | 312713 | 0.23% | 1732 |
| chr12 | 258324 | 0.19% | 1395 |
| chr13 | 93706 | 0.08% | 518 |
| chr14 | 173697 | 0.16% | 951 |
| chr15 | 163492 | 0.16% | 879 |
| chr16 | 229522 | 0.25% | 1248 |
| chr17 | 310097 | 0.37% | 1719 |
| chr18 | 94917 | 0.12% | 538 |
| chr19 | 369178 | 0.63% | 1881 |
| chr20 | 152835 | 0.24% | 882 |
| chr21 | 80485 | 0.17% | 467 |
| chr22 | 167732 | 0.33% | 961 |
| chrX | 115579 | 0.07% | 614 |
| chrY | 717 | <0.01% | 6 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 30103 | 1 | 760 | 181.13 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF865NAT.bed.gz | 327.86 KB | 5afcbd83466b50e7378337509e081a97 |
| ENCFF865NAT.tabix.bed.gz | 297.0 KB | 7c59b9bb8ed6c462071e469f06d196b4 |
| ENCFF865NAT.tabix.bed.gz.tbi | 158.69 KB | 1f837d496376a54f421e4d2af2474473 |
| genomic_resource.yaml | 2.25 KB | 66dfb31b4e8142a6c71f8e86a728a71b |
| statistics/ |