Resource
| Id | DNase-seq/ENCSR422PVL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR422PVL [biosample_summary="Homo sapiens left kidney tissue female embryo (147 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (147 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN603XNH|/analyses/ENCAN603XNH/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF159QUF|/files/ENCFF159QUF/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 29684986 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/}) audit_warning: Alignment file {ENCFF225BMQ|/files/ENCFF225BMQ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 29480912 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/}) 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 {ENCFF225BMQ|/files/ENCFF225BMQ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.31. 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR422PVL | float |
DNase-seq_ENCSR422PVL |
DNase-seq ENCSR422PVL [biosample_summary="Homo sapiens left kidney tissue female embryo (147 days)"]
|
 |
[4, 448] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8795416 | 0.27% | 58330 |
| chr1 | 789325 | 0.32% | 5242 |
| chr2 | 715329 | 0.30% | 4734 |
| chr3 | 586155 | 0.30% | 3897 |
| chr4 | 473175 | 0.25% | 3135 |
| chr5 | 488431 | 0.27% | 3237 |
| chr6 | 545019 | 0.32% | 3605 |
| chr7 | 441904 | 0.28% | 2927 |
| chr8 | 391426 | 0.27% | 2600 |
| chr9 | 376999 | 0.27% | 2503 |
| chr10 | 418170 | 0.31% | 2768 |
| chr11 | 459795 | 0.34% | 3047 |
| chr12 | 443546 | 0.33% | 2944 |
| chr13 | 244271 | 0.21% | 1611 |
| chr14 | 281321 | 0.26% | 1863 |
| chr15 | 285872 | 0.28% | 1898 |
| chr16 | 276917 | 0.31% | 1840 |
| chr17 | 339497 | 0.41% | 2257 |
| chr18 | 203117 | 0.25% | 1347 |
| chr19 | 320023 | 0.55% | 2124 |
| chr20 | 218471 | 0.34% | 1452 |
| chr21 | 96150 | 0.21% | 640 |
| chr22 | 145797 | 0.29% | 968 |
| chrX | 253806 | 0.16% | 1685 |
| chrY | 900 | <0.01% | 6 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 58330 | 28 | 450 | 150.79 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF281XUZ.bed.gz | 567.46 KB | e3a7716c57aaf57bcb3012fc4ced3534 |
| ENCFF281XUZ.tabix.bed.gz | 484.86 KB | 31cfc2748f0eb523a033bb25db7f8387 |
| ENCFF281XUZ.tabix.bed.gz.tbi | 323.75 KB | 345cbd0ae55cbafc47bcb98bbe0180ef |
| genomic_resource.yaml | 3.4 KB | e275f5a2f637f38a4fe1da446b769336 |
| statistics/ |