Resource
| Id | DNase-seq/ENCSR820WLP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR820WLP [biosample_summary="Homo sapiens dedifferentiated amniotic fluid mesenchymal stem cell male embryo (15 weeks)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (15 weeks) output_type: peaks audit_error: 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 {ENCFF833UTG|/files/ENCFF833UTG/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.22. 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_error: 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 {ENCFF381FQU|/files/ENCFF381FQU/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.18. 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_ENCSR820WLP | float |
DNase-seq_ENCSR820WLP |
DNase-seq ENCSR820WLP [biosample_summary="Homo sapiens dedifferentiated amniotic fluid mesenchymal stem cell male embryo (15 weeks)"]
|
 |
[0.0237, 9.69] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 20924102 | 0.65% | 117500 |
| chr1 | 1959786 | 0.79% | 10963 |
| chr2 | 1714096 | 0.71% | 9628 |
| chr3 | 1458752 | 0.74% | 8179 |
| chr4 | 1223439 | 0.64% | 7008 |
| chr5 | 1289541 | 0.71% | 7259 |
| chr6 | 1350369 | 0.79% | 7584 |
| chr7 | 1048015 | 0.66% | 5918 |
| chr8 | 1019366 | 0.70% | 5770 |
| chr9 | 890152 | 0.64% | 4970 |
| chr10 | 971099 | 0.73% | 5427 |
| chr11 | 1000699 | 0.74% | 5563 |
| chr12 | 1063215 | 0.80% | 5943 |
| chr13 | 540725 | 0.47% | 3094 |
| chr14 | 667278 | 0.62% | 3712 |
| chr15 | 670363 | 0.66% | 3742 |
| chr16 | 563379 | 0.62% | 3136 |
| chr17 | 823460 | 0.99% | 4529 |
| chr18 | 434847 | 0.54% | 2459 |
| chr19 | 649765 | 1.11% | 3461 |
| chr20 | 474441 | 0.74% | 2632 |
| chr21 | 251067 | 0.54% | 1420 |
| chr22 | 313666 | 0.62% | 1797 |
| chrX | 542012 | 0.35% | 3263 |
| chrY | 4570 | 0.01% | 43 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 117500 | 5 | 760 | 178.08 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF070COX.bed.gz | 1.26 MB | 6df793484eace5e3ab93e1ad4032a683 |
| ENCFF070COX.tabix.bed.gz | 1.15 MB | d40058d53df2496aca28dda0f1d08230 |
| ENCFF070COX.tabix.bed.gz.tbi | 459.95 KB | d123deccb5a7b9d30ad0ebab8bf6a43d |
| genomic_resource.yaml | 2.96 KB | 498503f646148d3f2063be9a827516c1 |
| statistics/ |