Resource
| Id | DNase-seq/ENCSR973MKT |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR973MKT [biosample_summary="Homo sapiens spinal cord tissue female embryo (87 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (87 days) output_type: peaks audit_warning: Alignment file {ENCFF963LSW|/files/ENCFF963LSW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 24741055 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 {ENCFF963LSW|/files/ENCFF963LSW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) 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-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR973MKT | float |
DNase-seq_ENCSR973MKT |
DNase-seq ENCSR973MKT [biosample_summary="Homo sapiens spinal cord tissue female embryo (87 days)"]
|
 |
[0.243, 16.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7486502 | 0.23% | 41694 |
| chr1 | 686044 | 0.28% | 3786 |
| chr2 | 571334 | 0.24% | 3233 |
| chr3 | 483370 | 0.24% | 2698 |
| chr4 | 385705 | 0.20% | 2157 |
| chr5 | 430753 | 0.24% | 2391 |
| chr6 | 445125 | 0.26% | 2479 |
| chr7 | 384623 | 0.24% | 2150 |
| chr8 | 329469 | 0.23% | 1859 |
| chr9 | 306966 | 0.22% | 1716 |
| chr10 | 324204 | 0.24% | 1873 |
| chr11 | 392264 | 0.29% | 2165 |
| chr12 | 375867 | 0.28% | 2091 |
| chr13 | 193184 | 0.17% | 1088 |
| chr14 | 242836 | 0.23% | 1331 |
| chr15 | 244484 | 0.24% | 1373 |
| chr16 | 254431 | 0.28% | 1417 |
| chr17 | 309686 | 0.37% | 1711 |
| chr18 | 149616 | 0.19% | 879 |
| chr19 | 362067 | 0.62% | 1844 |
| chr20 | 190305 | 0.30% | 1094 |
| chr21 | 83573 | 0.18% | 462 |
| chr22 | 122446 | 0.24% | 691 |
| chrX | 217416 | 0.14% | 1201 |
| chrY | 734 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41694 | 7 | 780 | 179.56 | 179 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF733BPU.bed.gz | 437.45 KB | 2e2d93735e1440d0b577890b78703848 |
| ENCFF733BPU.tabix.bed.gz | 390.19 KB | 7e1ffa7374879f386eccd625860045dd |
| ENCFF733BPU.tabix.bed.gz.tbi | 252.42 KB | 2ac08784f62f5520e6afc49c6aa64122 |
| genomic_resource.yaml | 2.66 KB | 167837f32c4a9cffb30e5963beee3075 |
| statistics/ |