Resource
| Id | DNase-seq/ENCSR663MNQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR663MNQ [biosample_summary="Homo sapiens with 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 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 {ENCFF108BWV|/files/ENCFF108BWV/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.30. 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_ENCSR663MNQ | float |
DNase-seq_ENCSR663MNQ |
DNase-seq ENCSR663MNQ [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.0575, 14.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 14090385 | 0.44% | 78253 |
| chr1 | 1376067 | 0.55% | 7569 |
| chr2 | 1036254 | 0.43% | 5857 |
| chr3 | 824193 | 0.42% | 4596 |
| chr4 | 568807 | 0.30% | 3157 |
| chr5 | 698960 | 0.39% | 3930 |
| chr6 | 762527 | 0.45% | 4247 |
| chr7 | 684832 | 0.43% | 3864 |
| chr8 | 591848 | 0.41% | 3300 |
| chr9 | 608293 | 0.44% | 3391 |
| chr10 | 683554 | 0.51% | 3816 |
| chr11 | 809817 | 0.60% | 4505 |
| chr12 | 695097 | 0.52% | 3797 |
| chr13 | 308990 | 0.27% | 1751 |
| chr14 | 456420 | 0.43% | 2552 |
| chr15 | 466765 | 0.46% | 2634 |
| chr16 | 565043 | 0.63% | 3137 |
| chr17 | 734878 | 0.88% | 4005 |
| chr18 | 257123 | 0.32% | 1480 |
| chr19 | 737988 | 1.26% | 3844 |
| chr20 | 406934 | 0.63% | 2291 |
| chr21 | 150127 | 0.32% | 828 |
| chr22 | 323345 | 0.64% | 1810 |
| chrX | 341961 | 0.22% | 1888 |
| chrY | 562 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 78253 | 1 | 860 | 180.06 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF803HTS.bed.gz | 861.78 KB | 00fb9550c54fe15b07b680785adc94cf |
| ENCFF803HTS.tabix.bed.gz | 784.74 KB | 5d135aa355c4434fcc28f0b445c6682a |
| ENCFF803HTS.tabix.bed.gz.tbi | 349.92 KB | 65935fe67a7c928bf5b7728c5573dbf9 |
| genomic_resource.yaml | 2.25 KB | 92987980c424bfda2023781257645309 |
| statistics/ |