Resource
| Id | DNase-seq/ENCSR000EPQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EPQ [biosample_summary="Homo sapiens keratinocyte female"] |
| Description |
status: released biological_replicates: Rep 1 summary: female output_type: peaks audit_warning: Replicate 2_1 has no significant footprints detected. audit_warning: Alignment file {ENCFF996YAL|/files/ENCFF996YAL/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 23796928 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: Alignment file {ENCFF142ZLU|/files/ENCFF142ZLU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 32152119 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 {ENCFF996YAL|/files/ENCFF996YAL/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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/}) 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 {ENCFF142ZLU|/files/ENCFF142ZLU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.28. 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_ENCSR000EPQ | float |
DNase-seq_ENCSR000EPQ |
DNase-seq ENCSR000EPQ [biosample_summary="Homo sapiens keratinocyte female"]
|
 |
[0.254, 20.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9271640 | 0.29% | 51542 |
| chr1 | 923439 | 0.37% | 5080 |
| chr2 | 766370 | 0.32% | 4293 |
| chr3 | 582650 | 0.29% | 3280 |
| chr4 | 456227 | 0.24% | 2589 |
| chr5 | 510294 | 0.28% | 2866 |
| chr6 | 569712 | 0.33% | 3173 |
| chr7 | 456718 | 0.29% | 2557 |
| chr8 | 418309 | 0.29% | 2338 |
| chr9 | 380643 | 0.28% | 2128 |
| chr10 | 432253 | 0.32% | 2419 |
| chr11 | 466422 | 0.35% | 2599 |
| chr12 | 480411 | 0.36% | 2647 |
| chr13 | 224818 | 0.20% | 1276 |
| chr14 | 295161 | 0.28% | 1627 |
| chr15 | 324948 | 0.32% | 1780 |
| chr16 | 298846 | 0.33% | 1645 |
| chr17 | 378097 | 0.45% | 2070 |
| chr18 | 208719 | 0.26% | 1196 |
| chr19 | 349785 | 0.60% | 1758 |
| chr20 | 247976 | 0.38% | 1377 |
| chr21 | 99501 | 0.21% | 562 |
| chr22 | 166466 | 0.33% | 933 |
| chrX | 233735 | 0.15% | 1348 |
| chrY | 140 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 51542 | 12 | 704 | 179.89 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF011WVC.bed.gz | 538.96 KB | 80124af6f8365e2453a3e3895ec90e28 |
| ENCFF011WVC.tabix.bed.gz | 478.02 KB | 036784f06b9c9ddee3d918dbb78cbd31 |
| ENCFF011WVC.tabix.bed.gz.tbi | 293.65 KB | 4672414900b215bad6fe9fbc225e474f |
| genomic_resource.yaml | 4.08 KB | 5dd83cea1107c085014867f8eb682197 |
| statistics/ |