Resource
| Id | DNase-seq/ENCSR949JYS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR949JYS [biosample_summary="Homo sapiens muscle of arm tissue male embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (105 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN561IBI|/analyses/ENCAN561IBI/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF641FDH|/files/ENCFF641FDH/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 35625295 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 {ENCFF999DLM|/files/ENCFF999DLM/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 35394128 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 {ENCFF999DLM|/files/ENCFF999DLM/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR949JYS | float |
DNase-seq_ENCSR949JYS |
DNase-seq ENCSR949JYS [biosample_summary="Homo sapiens muscle of arm tissue male embryo (105 days)"]
|
 |
[3, 482] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10935027 | 0.34% | 72357 |
| chr1 | 976575 | 0.39% | 6453 |
| chr2 | 871027 | 0.36% | 5755 |
| chr3 | 738324 | 0.37% | 4884 |
| chr4 | 608247 | 0.32% | 4026 |
| chr5 | 643017 | 0.35% | 4239 |
| chr6 | 706647 | 0.41% | 4674 |
| chr7 | 548367 | 0.34% | 3630 |
| chr8 | 516789 | 0.36% | 3420 |
| chr9 | 453680 | 0.33% | 3001 |
| chr10 | 523804 | 0.39% | 3469 |
| chr11 | 557110 | 0.41% | 3688 |
| chr12 | 541729 | 0.41% | 3586 |
| chr13 | 317872 | 0.28% | 2106 |
| chr14 | 372640 | 0.35% | 2474 |
| chr15 | 339612 | 0.33% | 2245 |
| chr16 | 316166 | 0.35% | 2095 |
| chr17 | 411887 | 0.49% | 2734 |
| chr18 | 250889 | 0.31% | 1664 |
| chr19 | 352505 | 0.60% | 2336 |
| chr20 | 266601 | 0.41% | 1761 |
| chr21 | 134913 | 0.29% | 892 |
| chr22 | 166530 | 0.33% | 1105 |
| chrX | 307196 | 0.20% | 2034 |
| chrY | 12900 | 0.02% | 86 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 72357 | 7 | 450 | 151.13 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF308QRZ.bed.gz | 690.74 KB | 6233f56e2da721d8672fd7af49691667 |
| ENCFF308QRZ.tabix.bed.gz | 591.58 KB | 77b89258c7d7418d7de88d8500a9540c |
| ENCFF308QRZ.tabix.bed.gz.tbi | 327.92 KB | 9cf790eee6f6d2cb3933fc67cca1f3d6 |
| genomic_resource.yaml | 3.4 KB | b203ce850d9d36fc827248b1d11a5708 |
| statistics/ |