Resource
| Id | DNase-seq/ENCSR411MGY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR411MGY [biosample_summary="Homo sapiens muscle of trunk tissue female embryo (121 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (121 days) output_type: peaks audit_warning: Alignment file {ENCFF793SQU|/files/ENCFF793SQU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 43388250 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 {ENCFF793SQU|/files/ENCFF793SQU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.36. 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_ENCSR411MGY | float |
DNase-seq_ENCSR411MGY |
DNase-seq ENCSR411MGY [biosample_summary="Homo sapiens muscle of trunk tissue female embryo (121 days)"]
|
 |
[0.185, 16.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 13439413 | 0.42% | 72267 |
| chr1 | 1198118 | 0.48% | 6418 |
| chr2 | 1085751 | 0.45% | 5859 |
| chr3 | 863611 | 0.44% | 4691 |
| chr4 | 697021 | 0.37% | 3757 |
| chr5 | 741603 | 0.41% | 4032 |
| chr6 | 815350 | 0.48% | 4332 |
| chr7 | 676718 | 0.42% | 3659 |
| chr8 | 642938 | 0.44% | 3464 |
| chr9 | 577303 | 0.42% | 3083 |
| chr10 | 653705 | 0.49% | 3531 |
| chr11 | 696995 | 0.52% | 3727 |
| chr12 | 683815 | 0.51% | 3654 |
| chr13 | 368676 | 0.32% | 2004 |
| chr14 | 432766 | 0.40% | 2310 |
| chr15 | 428503 | 0.42% | 2321 |
| chr16 | 406037 | 0.45% | 2214 |
| chr17 | 552943 | 0.66% | 2935 |
| chr18 | 289154 | 0.36% | 1579 |
| chr19 | 514959 | 0.88% | 2599 |
| chr20 | 345672 | 0.54% | 1895 |
| chr21 | 156040 | 0.33% | 845 |
| chr22 | 226641 | 0.45% | 1236 |
| chrX | 384792 | 0.25% | 2120 |
| chrY | 302 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 72267 | 2 | 780 | 185.97 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF014FUK.bed.gz | 762.6 KB | a07e2840f974f97f4be8b15010bfab76 |
| ENCFF014FUK.tabix.bed.gz | 686.26 KB | 66bd6a99f9aa60996fdf7148fa42c9aa |
| ENCFF014FUK.tabix.bed.gz.tbi | 371.66 KB | 5a5f75455fd6a335eb7b69a522a2c4f3 |
| genomic_resource.yaml | 2.68 KB | 1de6df37a0fbf6396894b8a9c40aebed |
| statistics/ |