Resource
| Id | DNase-seq/ENCSR452EGE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR452EGE [biosample_summary="Homo sapiens muscle of arm tissue male embryo (120 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (120 days) output_type: peaks audit_warning: Alignment file {ENCFF247QVO|/files/ENCFF247QVO/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 41136410 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 {ENCFF247QVO|/files/ENCFF247QVO/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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_ENCSR452EGE | float |
DNase-seq_ENCSR452EGE |
DNase-seq ENCSR452EGE [biosample_summary="Homo sapiens muscle of arm tissue male embryo (120 days)"]
|
 |
[0.195, 22.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12037466 | 0.37% | 63847 |
| chr1 | 1082223 | 0.43% | 5685 |
| chr2 | 970464 | 0.40% | 5160 |
| chr3 | 769022 | 0.39% | 4123 |
| chr4 | 628754 | 0.33% | 3345 |
| chr5 | 692426 | 0.38% | 3705 |
| chr6 | 755530 | 0.44% | 3980 |
| chr7 | 602962 | 0.38% | 3221 |
| chr8 | 572114 | 0.39% | 3031 |
| chr9 | 514932 | 0.37% | 2729 |
| chr10 | 584818 | 0.44% | 3123 |
| chr11 | 624402 | 0.46% | 3269 |
| chr12 | 611785 | 0.46% | 3189 |
| chr13 | 346082 | 0.30% | 1861 |
| chr14 | 390925 | 0.37% | 2061 |
| chr15 | 377865 | 0.37% | 2016 |
| chr16 | 353414 | 0.39% | 1891 |
| chr17 | 488291 | 0.59% | 2582 |
| chr18 | 263248 | 0.33% | 1430 |
| chr19 | 449584 | 0.77% | 2275 |
| chr20 | 287770 | 0.45% | 1561 |
| chr21 | 143013 | 0.31% | 750 |
| chr22 | 189993 | 0.37% | 1033 |
| chrX | 325807 | 0.21% | 1766 |
| chrY | 12042 | 0.02% | 61 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 63847 | 2 | 840 | 188.54 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF006YTP.bed.gz | 678.2 KB | 6efd6c3d3719849051d7bd9085a5ec34 |
| ENCFF006YTP.tabix.bed.gz | 609.01 KB | 11338cca8d52f1aa6e8e5dfae2fdff3a |
| ENCFF006YTP.tabix.bed.gz.tbi | 336.93 KB | 6bda24bf57311a2f777ac60d29781c90 |
| genomic_resource.yaml | 2.66 KB | 6d61b34388d03e04a79c4a03318c86fe |
| statistics/ |