Resource
| Id | DNase-seq/ENCSR532CRI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR532CRI [biosample_summary="Homo sapiens limb tissue embryo (58 days) and embryo (59 days)"] |
| Description |
status: released biological_replicates: Rep 2 summary: embryo (59 days) embryo (58 days) 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 {ENCFF371ZLX|/files/ENCFF371ZLX/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) for GRCh38 assembly have a SPOT1 score of 0.25. 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/}) audit_internal_action: Archived analysis {ENCAN929UJL|/analyses/ENCAN929UJL/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_not_compliant: Replicate concordance in DNase-seq experiments is measured by calculating the Pearson correlation between signal quantification of the replicates. ENCODE processed signal files {ENCFF850IPE|/files/ENCFF850IPE/}, {ENCFF135BMZ|/files/ENCFF135BMZ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) for GRCh38 assembly have a Pearson correlation of 0.83. According to ENCODE standards, in an anisogenic assay a Pearson correlation value > 0.85 is 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 {ENCFF757WSE|/files/ENCFF757WSE/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) for GRCh38 assembly have a SPOT1 score of 0.25. 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_ENCSR532CRI | float |
DNase-seq_ENCSR532CRI |
DNase-seq ENCSR532CRI [biosample_summary="Homo sapiens limb tissue embryo (58 days) and embryo (59 days)"]
|
 |
[7, 2.6e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 27909606 | 0.87% | 185708 |
| chr1 | 2418294 | 0.97% | 16096 |
| chr2 | 2323277 | 0.96% | 15461 |
| chr3 | 1882883 | 0.95% | 12533 |
| chr4 | 1594446 | 0.84% | 10610 |
| chr5 | 1637708 | 0.90% | 10892 |
| chr6 | 1719660 | 1.01% | 11440 |
| chr7 | 1431845 | 0.90% | 9527 |
| chr8 | 1388011 | 0.96% | 9235 |
| chr9 | 1183839 | 0.86% | 7872 |
| chr10 | 1407445 | 1.05% | 9370 |
| chr11 | 1371565 | 1.02% | 9125 |
| chr12 | 1353083 | 1.02% | 8995 |
| chr13 | 844377 | 0.74% | 5614 |
| chr14 | 896898 | 0.84% | 5967 |
| chr15 | 867419 | 0.85% | 5773 |
| chr16 | 821963 | 0.91% | 5473 |
| chr17 | 1016250 | 1.22% | 6764 |
| chr18 | 668204 | 0.83% | 4442 |
| chr19 | 749880 | 1.28% | 4991 |
| chr20 | 694414 | 1.08% | 4617 |
| chr21 | 335227 | 0.72% | 2233 |
| chr22 | 422756 | 0.83% | 2816 |
| chrX | 842714 | 0.54% | 5612 |
| chrY | 37448 | 0.07% | 250 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 185708 | 4 | 450 | 150.29 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF551YAW.bed.gz | 1.78 MB | 88c48fefb709b5083fc4e9099f637348 |
| ENCFF551YAW.tabix.bed.gz | 1.52 MB | 241c4470e26788ab8ccf20913dbcd681 |
| ENCFF551YAW.tabix.bed.gz.tbi | 661.29 KB | 63523992f93bc0699f85dfb929bab15e |
| genomic_resource.yaml | 3.64 KB | a78530093327cea837aa69182da17002 |
| statistics/ |