Resource
| Id | DNase-seq/ENCSR356QCD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR356QCD [biosample_summary="Homo sapiens muscle of arm tissue male embryo (101 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (101 days) output_type: peaks audit_warning: Alignment file {ENCFF656VNC|/files/ENCFF656VNC/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 20300900 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 {ENCFF656VNC|/files/ENCFF656VNC/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.32. 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_ENCSR356QCD | float |
DNase-seq_ENCSR356QCD |
DNase-seq ENCSR356QCD [biosample_summary="Homo sapiens muscle of arm tissue male embryo (101 days)"]
|
 |
[0.346, 12.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5406237 | 0.17% | 30057 |
| chr1 | 507232 | 0.20% | 2776 |
| chr2 | 422205 | 0.17% | 2359 |
| chr3 | 354997 | 0.18% | 2000 |
| chr4 | 263205 | 0.14% | 1482 |
| chr5 | 283187 | 0.16% | 1588 |
| chr6 | 324255 | 0.19% | 1817 |
| chr7 | 267738 | 0.17% | 1506 |
| chr8 | 237787 | 0.16% | 1359 |
| chr9 | 231370 | 0.17% | 1284 |
| chr10 | 240824 | 0.18% | 1383 |
| chr11 | 291405 | 0.22% | 1623 |
| chr12 | 286931 | 0.22% | 1549 |
| chr13 | 133986 | 0.12% | 759 |
| chr14 | 178345 | 0.17% | 961 |
| chr15 | 173752 | 0.17% | 972 |
| chr16 | 181267 | 0.20% | 996 |
| chr17 | 238213 | 0.29% | 1312 |
| chr18 | 104038 | 0.13% | 608 |
| chr19 | 279772 | 0.48% | 1414 |
| chr20 | 131859 | 0.20% | 754 |
| chr21 | 58440 | 0.13% | 322 |
| chr22 | 94911 | 0.19% | 538 |
| chrX | 115199 | 0.07% | 666 |
| chrY | 5319 | 0.01% | 29 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 30057 | 1 | 840 | 179.87 | 168 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF986SYJ.bed.gz | 311.4 KB | f72c20821ed5a77c1897cb84179e8ebb |
| ENCFF986SYJ.tabix.bed.gz | 276.73 KB | 9db8571440e2611671d00c47aa70c5c4 |
| ENCFF986SYJ.tabix.bed.gz.tbi | 194.23 KB | 09893c4770aa39ec975bdfc1a858fe0a |
| genomic_resource.yaml | 2.66 KB | 2d03ae790cef9356a16baf464aadaefe |
| statistics/ |