Resource
| Id | DNase-seq/ENCSR709PZI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR709PZI [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus 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 {ENCFF707REI|/files/ENCFF707REI/} processed by DNase-seq ENCODE4 v3.0.0 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_ENCSR709PZI | float |
DNase-seq_ENCSR709PZI |
DNase-seq ENCSR709PZI [biosample_summary="Homo sapiens with Alzheimer''s disease; posterior cingulate gyrus tissue female adult (88 years)"]
|
 |
[0.0329, 15.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 29935929 | 0.93% | 158752 |
| chr1 | 2841691 | 1.14% | 15067 |
| chr2 | 2456691 | 1.01% | 12981 |
| chr3 | 1426774 | 0.72% | 7628 |
| chr4 | 878676 | 0.46% | 4551 |
| chr5 | 1249478 | 0.69% | 6676 |
| chr6 | 1035200 | 0.61% | 5599 |
| chr7 | 1657335 | 1.04% | 8711 |
| chr8 | 1217901 | 0.84% | 6388 |
| chr9 | 1259040 | 0.91% | 6682 |
| chr10 | 1692756 | 1.27% | 9073 |
| chr11 | 1886363 | 1.40% | 9822 |
| chr12 | 1338408 | 1.00% | 7103 |
| chr13 | 465858 | 0.41% | 2489 |
| chr14 | 1048242 | 0.98% | 5546 |
| chr15 | 1141302 | 1.12% | 6100 |
| chr16 | 1468307 | 1.63% | 7827 |
| chr17 | 1875556 | 2.25% | 10010 |
| chr18 | 494380 | 0.62% | 2696 |
| chr19 | 1123657 | 1.92% | 5869 |
| chr20 | 1112756 | 1.73% | 5956 |
| chr21 | 483427 | 1.03% | 2578 |
| chr22 | 1266463 | 2.49% | 6644 |
| chrX | 513995 | 0.33% | 2743 |
| chrY | 1673 | <0.01% | 13 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 158752 | 1 | 920 | 188.57 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF653TDA.bed.gz | 1.54 MB | 0b45451f3105054c9eb6bd8f96a038d0 |
| ENCFF653TDA.tabix.bed.gz | 1.43 MB | fa75163cf9146f7b92e7027f6a45d925 |
| ENCFF653TDA.tabix.bed.gz.tbi | 278.1 KB | b757698d0e05a79534ba9298960755e1 |
| genomic_resource.yaml | 2.21 KB | 8eae8665eb4ed4d409eb54cafae56b1c |
| statistics/ |