Resource
| Id | DNase-seq/ENCSR355ARR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR355ARR [biosample_summary="Homo sapiens effector CD4-positive, alpha-beta T cell male adult (56 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (56 years) output_type: peaks audit_warning: Alignment file {ENCFF362PIS|/files/ENCFF362PIS/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 46820526 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 {ENCFF362PIS|/files/ENCFF362PIS/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR355ARR | float |
DNase-seq_ENCSR355ARR |
DNase-seq ENCSR355ARR [biosample_summary="Homo sapiens effector CD4-positive, alpha-beta T cell male adult (56 years)"]
|
 |
[0.278, 51.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4707916 | 0.15% | 25140 |
| chr1 | 503247 | 0.20% | 2683 |
| chr2 | 309017 | 0.13% | 1649 |
| chr3 | 243727 | 0.12% | 1308 |
| chr4 | 150102 | 0.08% | 801 |
| chr5 | 201399 | 0.11% | 1068 |
| chr6 | 267299 | 0.16% | 1439 |
| chr7 | 211231 | 0.13% | 1143 |
| chr8 | 162201 | 0.11% | 877 |
| chr9 | 183651 | 0.13% | 990 |
| chr10 | 189711 | 0.14% | 1025 |
| chr11 | 250152 | 0.19% | 1311 |
| chr12 | 252689 | 0.19% | 1348 |
| chr13 | 85351 | 0.07% | 455 |
| chr14 | 166026 | 0.16% | 894 |
| chr15 | 142017 | 0.14% | 779 |
| chr16 | 203248 | 0.22% | 1079 |
| chr17 | 301670 | 0.36% | 1636 |
| chr18 | 61813 | 0.08% | 329 |
| chr19 | 383129 | 0.65% | 1968 |
| chr20 | 130067 | 0.20% | 706 |
| chr21 | 54857 | 0.12% | 290 |
| chr22 | 113610 | 0.22% | 613 |
| chrX | 135922 | 0.09% | 717 |
| chrY | 5780 | 0.01% | 32 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 25140 | 3 | 680 | 187.27 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF972MAL.bed.gz | 282.31 KB | ec4cfaa60e83acf6c03a08827ff72a05 |
| ENCFF972MAL.tabix.bed.gz | 256.91 KB | 0942b6e659a92c2403fd2a76399231cf |
| ENCFF972MAL.tabix.bed.gz.tbi | 147.56 KB | 44f2cddb063cc02953249f7ebd8ed023 |
| genomic_resource.yaml | 2.72 KB | 72853b7c8a32a87f5584e15dba33b7b8 |
| statistics/ |