Resource
| Id | DNase-seq/ENCSR609DDQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR609DDQ [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell female adult (34 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (34 years) output_type: peaks audit_warning: Alignment file {ENCFF954LEK|/files/ENCFF954LEK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 23852858 mapped reads. According to ENCODE standards, conventional DNase-seq profile requires a minimum of 20 million uniquely mapped reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) 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 {ENCFF954LEK|/files/ENCFF954LEK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.29. 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_ENCSR609DDQ | float |
DNase-seq_ENCSR609DDQ |
DNase-seq ENCSR609DDQ [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell female adult (34 years)"]
|
 |
[0.379, 15.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5441236 | 0.17% | 27450 |
| chr1 | 549966 | 0.22% | 2740 |
| chr2 | 387928 | 0.16% | 1968 |
| chr3 | 328351 | 0.17% | 1639 |
| chr4 | 205124 | 0.11% | 1042 |
| chr5 | 256810 | 0.14% | 1314 |
| chr6 | 341590 | 0.20% | 1677 |
| chr7 | 265389 | 0.17% | 1337 |
| chr8 | 190801 | 0.13% | 1005 |
| chr9 | 209622 | 0.15% | 1104 |
| chr10 | 241013 | 0.18% | 1206 |
| chr11 | 282793 | 0.21% | 1430 |
| chr12 | 294967 | 0.22% | 1463 |
| chr13 | 112650 | 0.10% | 561 |
| chr14 | 187019 | 0.17% | 974 |
| chr15 | 166221 | 0.16% | 875 |
| chr16 | 207420 | 0.23% | 1048 |
| chr17 | 306941 | 0.37% | 1530 |
| chr18 | 80891 | 0.10% | 421 |
| chr19 | 342536 | 0.58% | 1613 |
| chr20 | 137898 | 0.21% | 733 |
| chr21 | 64346 | 0.14% | 317 |
| chr22 | 119346 | 0.23% | 617 |
| chrX | 161210 | 0.10% | 833 |
| chrY | 404 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 27450 | 3 | 998 | 198.22 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF566TYK.bed.gz | 288.69 KB | 102c5a3b765de086d58423a18ed6d14e |
| ENCFF566TYK.tabix.bed.gz | 259.52 KB | d9c313920878e363f48b60714349cf50 |
| ENCFF566TYK.tabix.bed.gz.tbi | 169.59 KB | 707d7a16f67c06680a6462b9477e382c |
| genomic_resource.yaml | 2.71 KB | 00c6bf176b8ae0564243704504d5dd8f |
| statistics/ |