Resource
| Id | DNase-seq/ENCSR437KLY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR437KLY [biosample_summary="Homo sapiens kidney tissue female embryo (85 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (85 days) output_type: peaks audit_warning: Alignment file {ENCFF667HRN|/files/ENCFF667HRN/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 36062889 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 {ENCFF667HRN|/files/ENCFF667HRN/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.28. 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_ENCSR437KLY | float |
DNase-seq_ENCSR437KLY |
DNase-seq ENCSR437KLY [biosample_summary="Homo sapiens kidney tissue female embryo (85 days)"]
|
 |
[0.251, 10.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5763931 | 0.18% | 30428 |
| chr1 | 551033 | 0.22% | 2831 |
| chr2 | 476175 | 0.20% | 2507 |
| chr3 | 389108 | 0.20% | 2019 |
| chr4 | 313268 | 0.16% | 1692 |
| chr5 | 328461 | 0.18% | 1763 |
| chr6 | 390619 | 0.23% | 2035 |
| chr7 | 280659 | 0.18% | 1527 |
| chr8 | 257720 | 0.18% | 1380 |
| chr9 | 224384 | 0.16% | 1205 |
| chr10 | 274676 | 0.21% | 1424 |
| chr11 | 288350 | 0.21% | 1515 |
| chr12 | 303089 | 0.23% | 1559 |
| chr13 | 155808 | 0.14% | 830 |
| chr14 | 192571 | 0.18% | 980 |
| chr15 | 181709 | 0.18% | 986 |
| chr16 | 159695 | 0.18% | 871 |
| chr17 | 207180 | 0.25% | 1115 |
| chr18 | 128201 | 0.16% | 690 |
| chr19 | 266299 | 0.45% | 1300 |
| chr20 | 120239 | 0.19% | 685 |
| chr21 | 58874 | 0.13% | 314 |
| chr22 | 73528 | 0.14% | 409 |
| chrX | 142038 | 0.09% | 789 |
| chrY | 247 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 30428 | 2 | 1140 | 189.43 | 176 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF234RER.bed.gz | 311.39 KB | 8d499a0811e0f19a6857c33714eca071 |
| ENCFF234RER.tabix.bed.gz | 280.43 KB | 0654ddddfb36e22397921f0c0e8aeef1 |
| ENCFF234RER.tabix.bed.gz.tbi | 180.1 KB | 94258e57f3e0333329c445685eb92aeb |
| genomic_resource.yaml | 2.65 KB | c62919213f0f123813f6e4f91349978e |
| statistics/ |