Resource
| Id | DNase-seq/ENCSR522FGG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR522FGG [biosample_summary="Homo sapiens stomach tissue male embryo (108 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (108 days) output_type: peaks audit_warning: Alignment file {ENCFF850NKJ|/files/ENCFF850NKJ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 20291832 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 {ENCFF850NKJ|/files/ENCFF850NKJ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.27. 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_ENCSR522FGG | float |
DNase-seq_ENCSR522FGG |
DNase-seq ENCSR522FGG [biosample_summary="Homo sapiens stomach tissue male embryo (108 days)"]
|
 |
[0.396, 12.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4958003 | 0.15% | 27840 |
| chr1 | 472452 | 0.19% | 2641 |
| chr2 | 368421 | 0.15% | 2093 |
| chr3 | 320139 | 0.16% | 1792 |
| chr4 | 224751 | 0.12% | 1272 |
| chr5 | 245905 | 0.14% | 1386 |
| chr6 | 290544 | 0.17% | 1651 |
| chr7 | 245181 | 0.15% | 1393 |
| chr8 | 214716 | 0.15% | 1225 |
| chr9 | 203414 | 0.15% | 1159 |
| chr10 | 218288 | 0.16% | 1245 |
| chr11 | 261216 | 0.19% | 1459 |
| chr12 | 258085 | 0.19% | 1435 |
| chr13 | 112300 | 0.10% | 642 |
| chr14 | 163498 | 0.15% | 916 |
| chr15 | 162287 | 0.16% | 926 |
| chr16 | 182005 | 0.20% | 1016 |
| chr17 | 231991 | 0.28% | 1293 |
| chr18 | 96341 | 0.12% | 559 |
| chr19 | 283483 | 0.48% | 1461 |
| chr20 | 139262 | 0.22% | 795 |
| chr21 | 54302 | 0.12% | 321 |
| chr22 | 102563 | 0.20% | 556 |
| chrX | 103114 | 0.07% | 583 |
| chrY | 3745 | 0.01% | 21 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 27840 | 1 | 880 | 178.09 | 161 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF078OQS.bed.gz | 288.21 KB | d979089785646965e91fe5e3297a9d5b |
| ENCFF078OQS.tabix.bed.gz | 256.64 KB | 88347e362ddcd73acca1350f4c55d389 |
| ENCFF078OQS.tabix.bed.gz.tbi | 180.97 KB | b4fe4d4b1e2499b3200ab7b3e652c93a |
| genomic_resource.yaml | 2.64 KB | a935c3acc004906eb22d1a1572296948 |
| statistics/ |