Resource
| Id | DNase-seq/ENCSR887BNC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR887BNC [biosample_summary="Homo sapiens right renal cortex interstitium tissue male embryo (120 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (120 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN942ASR|/analyses/ENCAN942ASR/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF886LAG|/files/ENCFF886LAG/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 28066043 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 {ENCFF967YWH|/files/ENCFF967YWH/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 27874865 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 {ENCFF967YWH|/files/ENCFF967YWH/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR887BNC | float |
DNase-seq_ENCSR887BNC |
DNase-seq ENCSR887BNC [biosample_summary="Homo sapiens right renal cortex interstitium tissue male embryo (120 days)"]
|
 |
[3, 391] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11201153 | 0.35% | 74357 |
| chr1 | 1002517 | 0.40% | 6659 |
| chr2 | 888764 | 0.37% | 5899 |
| chr3 | 748901 | 0.38% | 4963 |
| chr4 | 589791 | 0.31% | 3915 |
| chr5 | 627586 | 0.35% | 4166 |
| chr6 | 684167 | 0.40% | 4540 |
| chr7 | 574860 | 0.36% | 3817 |
| chr8 | 517722 | 0.36% | 3440 |
| chr9 | 450582 | 0.33% | 2993 |
| chr10 | 539894 | 0.40% | 3586 |
| chr11 | 571984 | 0.42% | 3795 |
| chr12 | 556994 | 0.42% | 3699 |
| chr13 | 319180 | 0.28% | 2116 |
| chr14 | 349925 | 0.33% | 2325 |
| chr15 | 355821 | 0.35% | 2352 |
| chr16 | 367077 | 0.41% | 2440 |
| chr17 | 455959 | 0.55% | 3032 |
| chr18 | 272700 | 0.34% | 1803 |
| chr19 | 405326 | 0.69% | 2695 |
| chr20 | 294250 | 0.46% | 1951 |
| chr21 | 126491 | 0.27% | 844 |
| chr22 | 189712 | 0.37% | 1260 |
| chrX | 300000 | 0.19% | 1994 |
| chrY | 10950 | 0.02% | 73 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 74357 | 19 | 450 | 150.64 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF883JEC.bed.gz | 717.79 KB | 5fee8c32b8fab202fb4704e56a23a1dc |
| ENCFF883JEC.tabix.bed.gz | 614.25 KB | 885e37ef9a99c9e5fccab5f77ffaf6c7 |
| ENCFF883JEC.tabix.bed.gz.tbi | 381.33 KB | e10a1e828abefade42e9a008dc85b888 |
| genomic_resource.yaml | 3.46 KB | 16f776daa070590ba7e70b7caee15beb |
| statistics/ |