Resource
| Id | DNase-seq/ENCSR249RFY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR249RFY [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 {ENCFF949QMT|/files/ENCFF949QMT/} processed by DNase-seq ENCODE4 v3.0.0 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_ENCSR249RFY | float |
DNase-seq_ENCSR249RFY |
DNase-seq ENCSR249RFY [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (90 or above years)"]
|
 |
[0.107, 10.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6099686 | 0.19% | 34072 |
| chr1 | 572936 | 0.23% | 3204 |
| chr2 | 483193 | 0.20% | 2783 |
| chr3 | 274704 | 0.14% | 1480 |
| chr4 | 179205 | 0.09% | 961 |
| chr5 | 238660 | 0.13% | 1351 |
| chr6 | 243799 | 0.14% | 1320 |
| chr7 | 274699 | 0.17% | 1542 |
| chr8 | 250032 | 0.17% | 1426 |
| chr9 | 291300 | 0.21% | 1625 |
| chr10 | 327661 | 0.24% | 1919 |
| chr11 | 392075 | 0.29% | 2195 |
| chr12 | 229062 | 0.17% | 1259 |
| chr13 | 87701 | 0.08% | 475 |
| chr14 | 206705 | 0.19% | 1157 |
| chr15 | 222370 | 0.22% | 1302 |
| chr16 | 254175 | 0.28% | 1419 |
| chr17 | 435171 | 0.52% | 2415 |
| chr18 | 118260 | 0.15% | 674 |
| chr19 | 382883 | 0.65% | 1968 |
| chr20 | 165836 | 0.26% | 941 |
| chr21 | 84605 | 0.18% | 512 |
| chr22 | 294504 | 0.58% | 1663 |
| chrX | 88474 | 0.06% | 469 |
| chrY | 1676 | <0.01% | 12 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 34072 | 3 | 800 | 179.02 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF475AVI.bed.gz | 352.37 KB | bd419c21713b5da07b5f00f26b379676 |
| ENCFF475AVI.tabix.bed.gz | 321.25 KB | 45b8ff7dd7aee02de9447e9c9a62057f |
| ENCFF475AVI.tabix.bed.gz.tbi | 135.77 KB | f80218bbf031a1c042cff2d3d1ce3c19 |
| genomic_resource.yaml | 2.25 KB | f94e0a9150e529ba6353382f5dcafeba |
| statistics/ |