Resource
| Id | DNase-seq/ENCSR775KLH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR775KLH [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue male adult (87 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (87 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 {ENCFF706MJM|/files/ENCFF706MJM/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR775KLH | float |
DNase-seq_ENCSR775KLH |
DNase-seq ENCSR775KLH [biosample_summary="Homo sapiens with Alzheimer''s disease; head of caudate nucleus tissue male adult (87 years)"]
|
 |
[0.0493, 21.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 16181822 | 0.50% | 85853 |
| chr1 | 1483875 | 0.60% | 7784 |
| chr2 | 1291284 | 0.53% | 6877 |
| chr3 | 903340 | 0.46% | 4799 |
| chr4 | 628449 | 0.33% | 3268 |
| chr5 | 820037 | 0.45% | 4373 |
| chr6 | 850150 | 0.50% | 4520 |
| chr7 | 783897 | 0.49% | 4163 |
| chr8 | 672067 | 0.46% | 3592 |
| chr9 | 719157 | 0.52% | 3822 |
| chr10 | 884251 | 0.66% | 4673 |
| chr11 | 913988 | 0.68% | 4831 |
| chr12 | 722129 | 0.54% | 3788 |
| chr13 | 366249 | 0.32% | 1954 |
| chr14 | 534065 | 0.50% | 2827 |
| chr15 | 554212 | 0.54% | 2961 |
| chr16 | 600889 | 0.67% | 3246 |
| chr17 | 797329 | 0.96% | 4247 |
| chr18 | 353352 | 0.44% | 1907 |
| chr19 | 796775 | 1.36% | 4172 |
| chr20 | 503124 | 0.78% | 2705 |
| chr21 | 174284 | 0.37% | 926 |
| chr22 | 410439 | 0.81% | 2188 |
| chrX | 401302 | 0.26% | 2137 |
| chrY | 17178 | 0.03% | 93 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 85853 | 1 | 960 | 188.48 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF691RHT.bed.gz | 944.48 KB | 6c59682847bc67ede6ecc8c31fb82e4e |
| ENCFF691RHT.tabix.bed.gz | 864.71 KB | 7199d0a706806de1b56b5b1d31878656 |
| ENCFF691RHT.tabix.bed.gz.tbi | 321.29 KB | 8428b6ded9287f66836f5b70c7e2df29 |
| genomic_resource.yaml | 2.2 KB | c8ce06296fc99fd3bf01848ac562a844 |
| statistics/ |