Resource
| Id | DNase-seq/ENCSR765BSU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR765BSU [biosample_summary="Homo sapiens right kidney tissue female embryo (117 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (117 days) output_type: peaks audit_warning: Alignment file {ENCFF907UIS|/files/ENCFF907UIS/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 34748745 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 {ENCFF907UIS|/files/ENCFF907UIS/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.33. 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_ENCSR765BSU | float |
DNase-seq_ENCSR765BSU |
DNase-seq ENCSR765BSU [biosample_summary="Homo sapiens right kidney tissue female embryo (117 days)"]
|
 |
[0.231, 12.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7593549 | 0.24% | 38635 |
| chr1 | 713380 | 0.29% | 3558 |
| chr2 | 594057 | 0.25% | 3031 |
| chr3 | 516656 | 0.26% | 2636 |
| chr4 | 414910 | 0.22% | 2097 |
| chr5 | 428144 | 0.24% | 2179 |
| chr6 | 495861 | 0.29% | 2446 |
| chr7 | 380160 | 0.24% | 1964 |
| chr8 | 321946 | 0.22% | 1725 |
| chr9 | 312201 | 0.23% | 1614 |
| chr10 | 343404 | 0.26% | 1800 |
| chr11 | 399095 | 0.30% | 2030 |
| chr12 | 387581 | 0.29% | 1912 |
| chr13 | 187141 | 0.16% | 946 |
| chr14 | 243852 | 0.23% | 1223 |
| chr15 | 249661 | 0.24% | 1273 |
| chr16 | 219643 | 0.24% | 1159 |
| chr17 | 298976 | 0.36% | 1486 |
| chr18 | 159593 | 0.20% | 831 |
| chr19 | 362915 | 0.62% | 1707 |
| chr20 | 173364 | 0.27% | 948 |
| chr21 | 75190 | 0.16% | 401 |
| chr22 | 113297 | 0.22% | 602 |
| chrX | 202295 | 0.13% | 1065 |
| chrY | 227 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 38635 | 1 | 940 | 196.55 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF939AKZ.bed.gz | 392.93 KB | 9ef1e4bea2eb31c0669edf340011c767 |
| ENCFF939AKZ.tabix.bed.gz | 356.97 KB | 709b41d9c749a8cc981dd2a5f1a310da |
| ENCFF939AKZ.tabix.bed.gz.tbi | 207.76 KB | 3c1c2b2a3e7af96c7438aa1da9b72111 |
| genomic_resource.yaml | 2.67 KB | 4400c29cdb6df96b49af6021193036e5 |
| statistics/ |