Resource
| Id | DNase-seq/ENCSR000EQH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EQH [biosample_summary="Homo sapiens T-helper 2 cell female adult (26 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (26 years) output_type: peaks audit_warning: Alignment file {ENCFF615FBZ|/files/ENCFF615FBZ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 28079837 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 {ENCFF615FBZ|/files/ENCFF615FBZ/} 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_ENCSR000EQH | float |
DNase-seq_ENCSR000EQH |
DNase-seq ENCSR000EQH [biosample_summary="Homo sapiens T-helper 2 cell female adult (26 years)"]
|
 |
[0.322, 28.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7606221 | 0.24% | 42489 |
| chr1 | 737909 | 0.30% | 4109 |
| chr2 | 583635 | 0.24% | 3278 |
| chr3 | 491084 | 0.25% | 2769 |
| chr4 | 323242 | 0.17% | 1829 |
| chr5 | 379464 | 0.21% | 2113 |
| chr6 | 477828 | 0.28% | 2659 |
| chr7 | 359485 | 0.23% | 2003 |
| chr8 | 305032 | 0.21% | 1743 |
| chr9 | 298765 | 0.22% | 1680 |
| chr10 | 354414 | 0.26% | 2007 |
| chr11 | 379233 | 0.28% | 2118 |
| chr12 | 392744 | 0.29% | 2183 |
| chr13 | 176433 | 0.15% | 966 |
| chr14 | 266222 | 0.25% | 1459 |
| chr15 | 239787 | 0.24% | 1355 |
| chr16 | 283421 | 0.31% | 1547 |
| chr17 | 385663 | 0.46% | 2134 |
| chr18 | 131858 | 0.16% | 760 |
| chr19 | 380522 | 0.65% | 2028 |
| chr20 | 186916 | 0.29% | 1080 |
| chr21 | 85563 | 0.18% | 490 |
| chr22 | 152637 | 0.30% | 865 |
| chrX | 234044 | 0.15% | 1312 |
| chrY | 320 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 42489 | 10 | 720 | 179.02 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF893DCZ.bed.gz | 452.34 KB | b058326896542fa1e20a1f947adabe91 |
| ENCFF893DCZ.tabix.bed.gz | 403.39 KB | b403e4e3328a028337842b09f976a229 |
| ENCFF893DCZ.tabix.bed.gz.tbi | 249.25 KB | c053d1f8591841da168a0111fe6470a8 |
| genomic_resource.yaml | 2.65 KB | 900f753e2ec501a26ccafb445ce480bb |
| statistics/ |