Resource
| Id | DNase-seq/ENCSR840TVG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR840TVG [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell female adult (33 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (33 years) output_type: peaks audit_warning: Replicate 1_2 has no significant footprints detected. audit_warning: Alignment file {ENCFF083TMS|/files/ENCFF083TMS/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 36299512 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 {ENCFF083TMS|/files/ENCFF083TMS/} 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_ENCSR840TVG | float |
DNase-seq_ENCSR840TVG |
DNase-seq ENCSR840TVG [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell female adult (33 years)"]
|
 |
[0.166, 12.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6364528 | 0.20% | 30860 |
| chr1 | 644619 | 0.26% | 3096 |
| chr2 | 466209 | 0.19% | 2270 |
| chr3 | 376683 | 0.19% | 1815 |
| chr4 | 248261 | 0.13% | 1182 |
| chr5 | 302488 | 0.17% | 1505 |
| chr6 | 390234 | 0.23% | 1856 |
| chr7 | 307859 | 0.19% | 1522 |
| chr8 | 224256 | 0.15% | 1115 |
| chr9 | 241491 | 0.17% | 1199 |
| chr10 | 282894 | 0.21% | 1413 |
| chr11 | 332216 | 0.25% | 1587 |
| chr12 | 337424 | 0.25% | 1598 |
| chr13 | 140435 | 0.12% | 681 |
| chr14 | 216352 | 0.20% | 1013 |
| chr15 | 201853 | 0.20% | 980 |
| chr16 | 241904 | 0.27% | 1177 |
| chr17 | 351735 | 0.42% | 1700 |
| chr18 | 100551 | 0.13% | 511 |
| chr19 | 405802 | 0.69% | 1866 |
| chr20 | 160708 | 0.25% | 825 |
| chr21 | 74618 | 0.16% | 364 |
| chr22 | 135424 | 0.27% | 690 |
| chrX | 180392 | 0.12% | 894 |
| chrY | 120 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 30860 | 5 | 960 | 206.24 | 193 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF953UPF.bed.gz | 324.32 KB | 4d1aabe576bcc983e2f6cfba0d72a0d7 |
| ENCFF953UPF.tabix.bed.gz | 294.82 KB | c1a1ed4199540358762a31d4c3ece488 |
| ENCFF953UPF.tabix.bed.gz.tbi | 176.29 KB | 1d5f61e9379b0bd574b3061541e2a0b0 |
| genomic_resource.yaml | 2.79 KB | 43a1bb88fea357b5da35c31fcc4bcea9 |
| statistics/ |