Resource
| Id | DNase-seq/ENCSR682PKY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR682PKY [biosample_summary="Homo sapiens thymus tissue female embryo"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo output_type: peaks audit_internal_action: Archived analysis {ENCAN519MPX|/analyses/ENCAN519MPX/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF810FRM|/files/ENCFF810FRM/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 32705402 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 {ENCFF139RJL|/files/ENCFF139RJL/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 32461431 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 {ENCFF139RJL|/files/ENCFF139RJL/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.40. 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_ENCSR682PKY | float |
DNase-seq_ENCSR682PKY |
DNase-seq ENCSR682PKY [biosample_summary="Homo sapiens thymus tissue female embryo"]
|
 |
[3, 1.36e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10774656 | 0.33% | 71704 |
| chr1 | 1015487 | 0.41% | 6756 |
| chr2 | 867613 | 0.36% | 5764 |
| chr3 | 693776 | 0.35% | 4617 |
| chr4 | 495561 | 0.26% | 3297 |
| chr5 | 544950 | 0.30% | 3628 |
| chr6 | 664044 | 0.39% | 4413 |
| chr7 | 526125 | 0.33% | 3502 |
| chr8 | 454500 | 0.31% | 3020 |
| chr9 | 435828 | 0.31% | 2903 |
| chr10 | 518170 | 0.39% | 3451 |
| chr11 | 504110 | 0.37% | 3359 |
| chr12 | 563177 | 0.42% | 3753 |
| chr13 | 278400 | 0.24% | 1846 |
| chr14 | 349597 | 0.33% | 2329 |
| chr15 | 340350 | 0.33% | 2266 |
| chr16 | 372150 | 0.41% | 2480 |
| chr17 | 509716 | 0.61% | 3397 |
| chr18 | 219750 | 0.27% | 1464 |
| chr19 | 449752 | 0.77% | 2997 |
| chr20 | 285181 | 0.44% | 1894 |
| chr21 | 133966 | 0.29% | 891 |
| chr22 | 218768 | 0.43% | 1458 |
| chrX | 317185 | 0.20% | 2109 |
| chrY | 16500 | 0.03% | 110 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 71704 | 36 | 339 | 150.27 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF186QHO.bed.gz | 699.61 KB | 681e22a3474d3fa7412091dd3bad1a4c |
| ENCFF186QHO.tabix.bed.gz | 602.27 KB | bbc0f3b390c9cc88584a096ddc8c98fc |
| ENCFF186QHO.tabix.bed.gz.tbi | 350.94 KB | 51f542f3d76064392eb5a19577fe8660 |
| genomic_resource.yaml | 3.33 KB | 5437b66b8534cf39d418871367cd6de4 |
| statistics/ |