Resource
| Id | DNase-seq/ENCSR788SOI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR788SOI [biosample_summary="Homo sapiens spinal cord tissue male embryo (96 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (96 days) output_type: peaks audit_warning: Alignment file {ENCFF556GYQ|/files/ENCFF556GYQ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 34786718 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 {ENCFF556GYQ|/files/ENCFF556GYQ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.30. 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_ENCSR788SOI | float |
DNase-seq_ENCSR788SOI |
DNase-seq ENCSR788SOI [biosample_summary="Homo sapiens spinal cord tissue male embryo (96 days)"]
|
 |
[0.231, 13.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8794138 | 0.27% | 46506 |
| chr1 | 810606 | 0.33% | 4279 |
| chr2 | 661600 | 0.27% | 3522 |
| chr3 | 599831 | 0.30% | 3157 |
| chr4 | 457007 | 0.24% | 2382 |
| chr5 | 487046 | 0.27% | 2575 |
| chr6 | 553715 | 0.32% | 2873 |
| chr7 | 472443 | 0.30% | 2481 |
| chr8 | 395494 | 0.27% | 2113 |
| chr9 | 361706 | 0.26% | 1932 |
| chr10 | 394080 | 0.29% | 2138 |
| chr11 | 450504 | 0.33% | 2378 |
| chr12 | 454067 | 0.34% | 2377 |
| chr13 | 227655 | 0.20% | 1219 |
| chr14 | 284972 | 0.27% | 1477 |
| chr15 | 292085 | 0.29% | 1552 |
| chr16 | 289374 | 0.32% | 1532 |
| chr17 | 361476 | 0.43% | 1926 |
| chr18 | 184406 | 0.23% | 1008 |
| chr19 | 388224 | 0.66% | 1956 |
| chr20 | 214398 | 0.33% | 1153 |
| chr21 | 90666 | 0.19% | 489 |
| chr22 | 140567 | 0.28% | 774 |
| chrX | 214295 | 0.14% | 1169 |
| chrY | 7921 | 0.01% | 44 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 46506 | 1 | 1020 | 189.1 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF112CXA.bed.gz | 481.79 KB | 6a480c862ee2dbf5b12358afcfef23e5 |
| ENCFF112CXA.tabix.bed.gz | 434.87 KB | 46da40b2afbb626f3cc9b98b4c972d29 |
| ENCFF112CXA.tabix.bed.gz.tbi | 258.59 KB | 67c5dfe2c64a0cfcfc184ac238b48c70 |
| genomic_resource.yaml | 2.65 KB | 638f765ad482c191025d0f033c9bcce9 |
| statistics/ |