Resource
| Id | DNase-seq/ENCSR970DQR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR970DQR [biosample_summary="Homo sapiens chondrocyte"] |
| Description |
status: released biological_replicates: Rep 2 summary: female embryo (5 days) 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 {ENCFF098QWQ|/files/ENCFF098QWQ/} processed by DNase-seq ENCODE4 v3.0.0 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/}) 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 {ENCFF099TKH|/files/ENCFF099TKH/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR970DQR | float |
DNase-seq_ENCSR970DQR |
DNase-seq ENCSR970DQR [biosample_summary="Homo sapiens chondrocyte"]
|
 |
[0.0444, 15.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 33587773 | 1.04% | 158319 |
| chr1 | 2839890 | 1.14% | 13250 |
| chr2 | 2497464 | 1.03% | 11698 |
| chr3 | 1468172 | 0.74% | 7056 |
| chr4 | 1176283 | 0.62% | 5502 |
| chr5 | 1425863 | 0.79% | 6782 |
| chr6 | 950178 | 0.56% | 4812 |
| chr7 | 2032841 | 1.28% | 9506 |
| chr8 | 1390223 | 0.96% | 6322 |
| chr9 | 1653798 | 1.19% | 7679 |
| chr10 | 1799842 | 1.35% | 8421 |
| chr11 | 2149347 | 1.59% | 9768 |
| chr12 | 1236154 | 0.93% | 5990 |
| chr13 | 471145 | 0.41% | 2359 |
| chr14 | 1128562 | 1.05% | 5299 |
| chr15 | 934483 | 0.92% | 4531 |
| chr16 | 1800985 | 1.99% | 8544 |
| chr17 | 2323409 | 2.79% | 11064 |
| chr18 | 391282 | 0.49% | 1917 |
| chr19 | 1361041 | 2.32% | 6464 |
| chr20 | 1313572 | 2.04% | 6097 |
| chr21 | 666088 | 1.43% | 3011 |
| chr22 | 1695585 | 3.34% | 7674 |
| chrX | 878648 | 0.56% | 4548 |
| chrY | 2918 | 0.01% | 25 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 158319 | 1 | 1200 | 212.15 | 198 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF429PXE.bed.gz | 1.45 MB | b5c45f5105517b46f976ace29b123548 |
| ENCFF429PXE.tabix.bed.gz | 1.4 MB | ab101c4694828bd06074c96b6fddaef0 |
| ENCFF429PXE.tabix.bed.gz.tbi | 218.38 KB | 543855e743764a6d850f1a66afb2958d |
| genomic_resource.yaml | 2.77 KB | 8c3a52a1f32b462f7b1a39265a6dfe03 |
| statistics/ |