Resource
| Id | DNase-seq/ENCSR763XBU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR763XBU [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (88 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (88 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 {ENCFF277BCT|/files/ENCFF277BCT/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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_ENCSR763XBU | float |
DNase-seq_ENCSR763XBU |
DNase-seq ENCSR763XBU [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (88 years)"]
|
 |
[0.123, 14] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7329647 | 0.23% | 39563 |
| chr1 | 666270 | 0.27% | 3620 |
| chr2 | 507892 | 0.21% | 2769 |
| chr3 | 376071 | 0.19% | 2036 |
| chr4 | 287226 | 0.15% | 1535 |
| chr5 | 327725 | 0.18% | 1806 |
| chr6 | 335918 | 0.20% | 1807 |
| chr7 | 374716 | 0.24% | 2011 |
| chr8 | 366138 | 0.25% | 1991 |
| chr9 | 329651 | 0.24% | 1804 |
| chr10 | 340395 | 0.25% | 1868 |
| chr11 | 429937 | 0.32% | 2332 |
| chr12 | 343815 | 0.26% | 1828 |
| chr13 | 128346 | 0.11% | 681 |
| chr14 | 252093 | 0.24% | 1361 |
| chr15 | 209939 | 0.21% | 1153 |
| chr16 | 282937 | 0.31% | 1495 |
| chr17 | 417126 | 0.50% | 2248 |
| chr18 | 120285 | 0.15% | 676 |
| chr19 | 451184 | 0.77% | 2300 |
| chr20 | 226043 | 0.35% | 1250 |
| chr21 | 108178 | 0.23% | 585 |
| chr22 | 278043 | 0.55% | 1531 |
| chrX | 169107 | 0.11% | 871 |
| chrY | 612 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 39563 | 4 | 840 | 185.27 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF391XXF.bed.gz | 431.82 KB | ef7d9c9d35f12a73a792b2c14f97a776 |
| ENCFF391XXF.tabix.bed.gz | 390.94 KB | 74ae30cdb3cab66193b326dbea611d71 |
| ENCFF391XXF.tabix.bed.gz.tbi | 187.49 KB | e84c8141fda028db5310186811780631 |
| genomic_resource.yaml | 2.23 KB | 12b27ae51dbc3fc4e261638c037773f4 |
| statistics/ |