Resource
| Id | DNase-seq/ENCSR124IMM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR124IMM [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex 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 {ENCFF063HKZ|/files/ENCFF063HKZ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.27. 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_ENCSR124IMM | float |
DNase-seq_ENCSR124IMM |
DNase-seq ENCSR124IMM [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (90 or above years)"]
|
 |
[0.0733, 13.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10923596 | 0.34% | 62184 |
| chr1 | 1003783 | 0.40% | 5692 |
| chr2 | 889856 | 0.37% | 5172 |
| chr3 | 599022 | 0.30% | 3444 |
| chr4 | 395512 | 0.21% | 2243 |
| chr5 | 554641 | 0.31% | 3198 |
| chr6 | 546785 | 0.32% | 3140 |
| chr7 | 536254 | 0.34% | 3071 |
| chr8 | 460655 | 0.32% | 2664 |
| chr9 | 499096 | 0.36% | 2821 |
| chr10 | 537545 | 0.40% | 3107 |
| chr11 | 627849 | 0.46% | 3560 |
| chr12 | 501574 | 0.38% | 2835 |
| chr13 | 202476 | 0.18% | 1191 |
| chr14 | 359692 | 0.34% | 2054 |
| chr15 | 396726 | 0.39% | 2252 |
| chr16 | 422009 | 0.47% | 2363 |
| chr17 | 573124 | 0.69% | 3217 |
| chr18 | 201134 | 0.25% | 1208 |
| chr19 | 579693 | 0.99% | 3069 |
| chr20 | 345274 | 0.54% | 1966 |
| chr21 | 130441 | 0.28% | 752 |
| chr22 | 331169 | 0.65% | 1889 |
| chrX | 228583 | 0.15% | 1270 |
| chrY | 703 | <0.01% | 6 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 62184 | 1 | 760 | 175.67 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF735SHW.bed.gz | 678.42 KB | 8dfb2754376e47335fe52eea150c16cc |
| ENCFF735SHW.tabix.bed.gz | 615.27 KB | 5bbf9e6f1dcaa4ecbf56a383aca15706 |
| ENCFF735SHW.tabix.bed.gz.tbi | 281.49 KB | 56bb39cef8e74a83220f4c45b21c7a79 |
| genomic_resource.yaml | 2.28 KB | 6d47ee779ac45878c1d2a3e58954ef21 |
| statistics/ |