Resource
| Id | DNase-seq/ENCSR962EAP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR962EAP [biosample_summary="Homo sapiens thymus tissue male embryo (104 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (104 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN031DGQ|/analyses/ENCAN031DGQ/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF287NZN|/files/ENCFF287NZN/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 46608711 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/}) audit_warning: Alignment file {ENCFF483PTN|/files/ENCFF483PTN/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 46246512 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/}) 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 {ENCFF483PTN|/files/ENCFF483PTN/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR962EAP | float |
DNase-seq_ENCSR962EAP |
DNase-seq ENCSR962EAP [biosample_summary="Homo sapiens thymus tissue male embryo (104 days)"]
|
 |
[4, 1.34e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12543974 | 0.39% | 83367 |
| chr1 | 1185070 | 0.48% | 7867 |
| chr2 | 1002300 | 0.41% | 6675 |
| chr3 | 826900 | 0.42% | 5488 |
| chr4 | 586700 | 0.31% | 3890 |
| chr5 | 647875 | 0.36% | 4297 |
| chr6 | 761464 | 0.45% | 5063 |
| chr7 | 624828 | 0.39% | 4148 |
| chr8 | 525402 | 0.36% | 3490 |
| chr9 | 516036 | 0.37% | 3430 |
| chr10 | 599041 | 0.45% | 3980 |
| chr11 | 587839 | 0.44% | 3908 |
| chr12 | 639372 | 0.48% | 4254 |
| chr13 | 337641 | 0.30% | 2238 |
| chr14 | 429305 | 0.40% | 2852 |
| chr15 | 411075 | 0.40% | 2733 |
| chr16 | 425768 | 0.47% | 2834 |
| chr17 | 581057 | 0.70% | 3870 |
| chr18 | 249442 | 0.31% | 1661 |
| chr19 | 495983 | 0.85% | 3305 |
| chr20 | 325629 | 0.51% | 2168 |
| chr21 | 152833 | 0.33% | 1017 |
| chr22 | 241409 | 0.48% | 1606 |
| chrX | 369588 | 0.24% | 2451 |
| chrY | 21417 | 0.04% | 142 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 83367 | 18 | 446 | 150.47 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF945ILS.bed.gz | 808.49 KB | b176b352e7aceb4b8fcad095babcae66 |
| ENCFF945ILS.tabix.bed.gz | 695.96 KB | a15a6a4af16963a2552deb9d5d3580bd |
| ENCFF945ILS.tabix.bed.gz.tbi | 365.33 KB | 2b3e3754e41c66362db5db6ef69d8775 |
| genomic_resource.yaml | 3.38 KB | a84ff66113575b02961660707c4ddb9c |
| statistics/ |