Resource
| Id | DNase-seq/ENCSR224IYD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR224IYD [biosample_summary="Homo sapiens medulla oblongata tissue male adult (78 years) and male adult (84 years)"] |
| Description |
status: released biological_replicates: Rep 2 summary: male adult (84 years) male adult (78 years) output_type: peaks audit_error: 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 {ENCFF182IAY|/files/ENCFF182IAY/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.17. 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/}) audit_error: 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 {ENCFF188LQX|/files/ENCFF188LQX/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.21. 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/}) audit_internal_action: Archived analysis {ENCAN284HPJ|/analyses/ENCAN284HPJ/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR224IYD | float |
DNase-seq_ENCSR224IYD |
DNase-seq ENCSR224IYD [biosample_summary="Homo sapiens medulla oblongata tissue male adult (78 years) and male adult (84 years)"]
|
 |
[5, 7.79e+04] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 37398570 | 1.16% | 248945 |
| chr1 | 3465213 | 1.39% | 23068 |
| chr2 | 3046253 | 1.26% | 20282 |
| chr3 | 2472167 | 1.25% | 16454 |
| chr4 | 1881576 | 0.99% | 12516 |
| chr5 | 2096266 | 1.15% | 13958 |
| chr6 | 2169410 | 1.27% | 14450 |
| chr7 | 1908778 | 1.20% | 12702 |
| chr8 | 1682412 | 1.16% | 11195 |
| chr9 | 1663568 | 1.20% | 11071 |
| chr10 | 1850331 | 1.38% | 12317 |
| chr11 | 1865874 | 1.38% | 12412 |
| chr12 | 1799172 | 1.35% | 11973 |
| chr13 | 1029457 | 0.90% | 6848 |
| chr14 | 1211892 | 1.13% | 8073 |
| chr15 | 1194790 | 1.17% | 7956 |
| chr16 | 1225662 | 1.36% | 8161 |
| chr17 | 1528155 | 1.84% | 10174 |
| chr18 | 885457 | 1.10% | 5893 |
| chr19 | 1085034 | 1.85% | 7231 |
| chr20 | 985203 | 1.53% | 6560 |
| chr21 | 484077 | 1.04% | 3225 |
| chr22 | 675169 | 1.33% | 4494 |
| chrX | 1105054 | 0.71% | 7348 |
| chrY | 87600 | 0.15% | 584 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 248945 | 1 | 450 | 150.23 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF356BZZ.bed.gz | 2.39 MB | cccca8600b119ca84a6cb18bfda9ec83 |
| ENCFF356BZZ.tabix.bed.gz | 2.06 MB | ed5064a9bdcaa28af47f62742d5fa79b |
| ENCFF356BZZ.tabix.bed.gz.tbi | 680.31 KB | 53e73ff8752f56cd9bd57693bfa61d70 |
| genomic_resource.yaml | 3.13 KB | 7fd76c2029891c228bb60be0c7391055 |
| statistics/ |