Resource
| Id | DNase-seq/ENCSR000EMJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EMJ [biosample_summary="Homo sapiens B cell female adult (43 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (43 years) output_type: peaks audit_internal_action: Archived analysis {ENCAN556ZAU|/analyses/ENCAN556ZAU/} 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 {ENCFF801IWM|/files/ENCFF801IWM/}, {ENCFF305QCJ|/files/ENCFF305QCJ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a Pearson correlation of 0.89. According to ENCODE standards, in an isogenic assay a Pearson correlation value > 0.9 is recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq/} ) audit_warning: Alignment file {ENCFF210XND|/files/ENCFF210XND/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 33733574 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000EMJ | float |
DNase-seq_ENCSR000EMJ |
DNase-seq ENCSR000EMJ [biosample_summary="Homo sapiens B cell female adult (43 years)"]
|
 |
[3, 2.09e+04] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 22094721 | 0.69% | 146940 |
| chr1 | 2056515 | 0.83% | 13679 |
| chr2 | 1695762 | 0.70% | 11268 |
| chr3 | 1297767 | 0.65% | 8621 |
| chr4 | 982317 | 0.52% | 6522 |
| chr5 | 1139061 | 0.63% | 7573 |
| chr6 | 1348702 | 0.79% | 8968 |
| chr7 | 1109780 | 0.70% | 7365 |
| chr8 | 959173 | 0.66% | 6380 |
| chr9 | 916042 | 0.66% | 6101 |
| chr10 | 989225 | 0.74% | 6578 |
| chr11 | 1104642 | 0.82% | 7352 |
| chr12 | 1091808 | 0.82% | 7269 |
| chr13 | 535953 | 0.47% | 3557 |
| chr14 | 738805 | 0.69% | 4913 |
| chr15 | 686645 | 0.67% | 4571 |
| chr16 | 780343 | 0.86% | 5189 |
| chr17 | 1091081 | 1.31% | 7261 |
| chr18 | 444638 | 0.55% | 2960 |
| chr19 | 1093341 | 1.87% | 7275 |
| chr20 | 574004 | 0.89% | 3822 |
| chr21 | 242929 | 0.52% | 1620 |
| chr22 | 482766 | 0.95% | 3213 |
| chrX | 728922 | 0.47% | 4853 |
| chrY | 4500 | 0.01% | 30 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 146940 | 3 | 450 | 150.37 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF541VKE.bed.gz | 1.42 MB | 00562290cbbe755d86f7701a4cd099c9 |
| ENCFF541VKE.tabix.bed.gz | 1.22 MB | 0ff7a183c21a0707f3f147fc3c38b549 |
| ENCFF541VKE.tabix.bed.gz.tbi | 482.26 KB | 0eef197e018b31ed03753c411a47f4b6 |
| genomic_resource.yaml | 2.56 KB | 8734d1308bcc267994be8a7362d8fb8e |
| statistics/ |