Resource
| Id | DNase-seq/ENCSR964MZQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR964MZQ [biosample_summary="Homo sapiens trophoblast cell embryo (39 weeks) and embryo (40 weeks)"] |
| Description |
status: released biological_replicates: Rep 1 summary: embryo (40 weeks) embryo (39 weeks) output_type: peaks 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 {ENCFF809XEZ|/files/ENCFF809XEZ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.32. 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_ENCSR964MZQ | float |
DNase-seq_ENCSR964MZQ |
DNase-seq ENCSR964MZQ [biosample_summary="Homo sapiens trophoblast cell embryo (39 weeks) and embryo (40 weeks)"]
|
 |
[0.029, 12.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 44114921 | 1.37% | 219240 |
| chr1 | 4227834 | 1.70% | 20999 |
| chr2 | 3531144 | 1.46% | 17549 |
| chr3 | 2944916 | 1.49% | 14723 |
| chr4 | 2265223 | 1.19% | 11358 |
| chr5 | 2486774 | 1.37% | 12351 |
| chr6 | 2880577 | 1.69% | 14184 |
| chr7 | 2321122 | 1.46% | 11593 |
| chr8 | 1974973 | 1.36% | 9800 |
| chr9 | 1869770 | 1.35% | 9342 |
| chr10 | 2062587 | 1.54% | 10254 |
| chr11 | 2191711 | 1.62% | 10855 |
| chr12 | 2189904 | 1.64% | 10879 |
| chr13 | 1113883 | 0.97% | 5520 |
| chr14 | 1333185 | 1.25% | 6567 |
| chr15 | 1402829 | 1.38% | 6959 |
| chr16 | 1325251 | 1.47% | 6596 |
| chr17 | 1764915 | 2.12% | 8760 |
| chr18 | 961364 | 1.20% | 4791 |
| chr19 | 1516834 | 2.59% | 7345 |
| chr20 | 1068569 | 1.66% | 5339 |
| chr21 | 512545 | 1.10% | 2504 |
| chr22 | 752572 | 1.48% | 3739 |
| chrX | 1313511 | 0.84% | 6686 |
| chrY | 102928 | 0.18% | 547 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 219240 | 1 | 980 | 201.22 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF619GCA.bed.gz | 2.34 MB | 21b0fd607ac3e68ff1dda09d303e684e |
| ENCFF619GCA.tabix.bed.gz | 2.14 MB | 476a11f16a93b6a75a64482cdaa982af |
| ENCFF619GCA.tabix.bed.gz.tbi | 648.08 KB | b2096491b3ee85b91cd9120538eca305 |
| genomic_resource.yaml | 2.11 KB | 1643499427dd8df19e017ab4b332c41f |
| statistics/ |