Resource
| Id | DNase-seq/ENCSR000FEK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000FEK [biosample_summary="Homo sapiens SK-MEL-5"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: peaks audit_warning: Alignment file {ENCFF207FFJ|/files/ENCFF207FFJ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 37564407 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 {ENCFF207FFJ|/files/ENCFF207FFJ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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_ENCSR000FEK | float |
DNase-seq_ENCSR000FEK |
DNase-seq ENCSR000FEK [biosample_summary="Homo sapiens SK-MEL-5"]
|
 |
[0.0284, 43] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 32568694 | 1.01% | 168409 |
| chr1 | 2827932 | 1.14% | 14682 |
| chr2 | 2619874 | 1.08% | 13551 |
| chr3 | 2144896 | 1.08% | 11056 |
| chr4 | 1713274 | 0.90% | 8954 |
| chr5 | 1911139 | 1.05% | 9861 |
| chr6 | 2118186 | 1.24% | 10722 |
| chr7 | 1870681 | 1.17% | 9618 |
| chr8 | 1606646 | 1.11% | 8253 |
| chr9 | 1295003 | 0.94% | 6694 |
| chr10 | 1395705 | 1.04% | 7253 |
| chr11 | 1558629 | 1.15% | 8094 |
| chr12 | 1706932 | 1.28% | 8761 |
| chr13 | 1009794 | 0.88% | 5205 |
| chr14 | 1007525 | 0.94% | 5222 |
| chr15 | 1040139 | 1.02% | 5402 |
| chr16 | 918760 | 1.02% | 4820 |
| chr17 | 1336024 | 1.60% | 6856 |
| chr18 | 704508 | 0.88% | 3669 |
| chr19 | 948163 | 1.62% | 4878 |
| chr20 | 857276 | 1.33% | 4460 |
| chr21 | 354820 | 0.76% | 1828 |
| chr22 | 553207 | 1.09% | 2914 |
| chrX | 1067921 | 0.68% | 5645 |
| chrY | 1660 | <0.01% | 11 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 168409 | 3 | 880 | 193.39 | 189 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF659HYC.bed.gz | 1.83 MB | b28a2082094c7047df74fdee03a5cf5b |
| ENCFF659HYC.tabix.bed.gz | 1.67 MB | fc1c2f49dae580d9369561671c6e0f7a |
| ENCFF659HYC.tabix.bed.gz.tbi | 629.97 KB | 446588ebf08046afa5d1a3e247ad3a93 |
| genomic_resource.yaml | 2.56 KB | 7f4deabb40848b111da71b9171077a01 |
| statistics/ |