Resource
| Id | DNase-seq/ENCSR016THC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR016THC [biosample_summary="Homo sapiens left renal pelvis tissue male embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (105 days) output_type: peaks audit_warning: Alignment file {ENCFF728YQN|/files/ENCFF728YQN/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 27567783 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 {ENCFF728YQN|/files/ENCFF728YQN/} 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_ENCSR016THC | float |
DNase-seq_ENCSR016THC |
DNase-seq ENCSR016THC [biosample_summary="Homo sapiens left renal pelvis tissue male embryo (105 days)"]
|
 |
[0.255, 15.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6802308 | 0.21% | 35142 |
| chr1 | 632319 | 0.25% | 3189 |
| chr2 | 523051 | 0.22% | 2740 |
| chr3 | 445559 | 0.22% | 2317 |
| chr4 | 352705 | 0.19% | 1787 |
| chr5 | 373737 | 0.21% | 1960 |
| chr6 | 437777 | 0.26% | 2230 |
| chr7 | 342429 | 0.21% | 1817 |
| chr8 | 285710 | 0.20% | 1533 |
| chr9 | 273246 | 0.20% | 1445 |
| chr10 | 327134 | 0.24% | 1703 |
| chr11 | 355120 | 0.26% | 1835 |
| chr12 | 360712 | 0.27% | 1866 |
| chr13 | 171731 | 0.15% | 901 |
| chr14 | 223326 | 0.21% | 1134 |
| chr15 | 217567 | 0.21% | 1120 |
| chr16 | 215110 | 0.24% | 1130 |
| chr17 | 273560 | 0.33% | 1402 |
| chr18 | 147253 | 0.18% | 780 |
| chr19 | 340276 | 0.58% | 1581 |
| chr20 | 160489 | 0.25% | 889 |
| chr21 | 71178 | 0.15% | 366 |
| chr22 | 104034 | 0.20% | 544 |
| chrX | 160800 | 0.10% | 840 |
| chrY | 7485 | 0.01% | 33 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 35142 | 2 | 1100 | 193.57 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF289MVB.bed.gz | 364.41 KB | 0ed6ed7e4060c24cae33564adc1dab18 |
| ENCFF289MVB.tabix.bed.gz | 328.06 KB | f31d5eb55bd080f11684e58631afcb4c |
| ENCFF289MVB.tabix.bed.gz.tbi | 201.42 KB | aecf82df0698046eba3a850c3d023da2 |
| genomic_resource.yaml | 2.67 KB | ccea3cc82b91344e9a5c0ab8b6c4eede |
| statistics/ |