Resource
| Id | DNase-seq/ENCSR033DQS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR033DQS [biosample_summary="Homo sapiens muscle of leg tissue male embryo (97 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (97 days) output_type: peaks audit_warning: Replicate 1_3 has no significant footprints detected. audit_warning: Alignment file {ENCFF951SGI|/files/ENCFF951SGI/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 31073461 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 {ENCFF951SGI|/files/ENCFF951SGI/} 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_ENCSR033DQS | float |
DNase-seq_ENCSR033DQS |
DNase-seq ENCSR033DQS [biosample_summary="Homo sapiens muscle of leg tissue male embryo (97 days)"]
|
 |
[0.161, 17.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9261842 | 0.29% | 50196 |
| chr1 | 855052 | 0.34% | 4563 |
| chr2 | 744411 | 0.31% | 4078 |
| chr3 | 619035 | 0.31% | 3356 |
| chr4 | 485119 | 0.26% | 2656 |
| chr5 | 514810 | 0.28% | 2809 |
| chr6 | 576629 | 0.34% | 3094 |
| chr7 | 444612 | 0.28% | 2439 |
| chr8 | 427447 | 0.29% | 2341 |
| chr9 | 394324 | 0.28% | 2147 |
| chr10 | 423472 | 0.32% | 2329 |
| chr11 | 480089 | 0.36% | 2572 |
| chr12 | 478027 | 0.36% | 2568 |
| chr13 | 253939 | 0.22% | 1376 |
| chr14 | 302431 | 0.28% | 1633 |
| chr15 | 298237 | 0.29% | 1596 |
| chr16 | 284139 | 0.31% | 1559 |
| chr17 | 380239 | 0.46% | 2070 |
| chr18 | 201328 | 0.25% | 1119 |
| chr19 | 382735 | 0.65% | 1940 |
| chr20 | 233233 | 0.36% | 1296 |
| chr21 | 103855 | 0.22% | 572 |
| chr22 | 152045 | 0.30% | 826 |
| chrX | 218204 | 0.14% | 1216 |
| chrY | 8430 | 0.01% | 41 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 50196 | 2 | 860 | 184.51 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF348ZJB.bed.gz | 526.19 KB | c32acb1c0c6875f87dda3342eddb1f3b |
| ENCFF348ZJB.tabix.bed.gz | 470.45 KB | dc6a3f70590a8fd92041bf43e96574b7 |
| ENCFF348ZJB.tabix.bed.gz.tbi | 283.63 KB | 03cdea71936a7b7f14be967abc5a7ba7 |
| genomic_resource.yaml | 2.74 KB | 903418968adf61290d20ad033353c15d |
| statistics/ |