Resource
| Id | DNase-seq/ENCSR278FHC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR278FHC [biosample_summary="Homo sapiens testis tissue male embryo"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo output_type: peaks audit_warning: Alignment file {ENCFF771NTS|/files/ENCFF771NTS/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 25806247 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 {ENCFF771NTS|/files/ENCFF771NTS/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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_ENCSR278FHC | float |
DNase-seq_ENCSR278FHC |
DNase-seq ENCSR278FHC [biosample_summary="Homo sapiens testis tissue male embryo"]
|
 |
[0.272, 30] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8082293 | 0.25% | 43715 |
| chr1 | 754650 | 0.30% | 4042 |
| chr2 | 624873 | 0.26% | 3393 |
| chr3 | 546368 | 0.28% | 2980 |
| chr4 | 424094 | 0.22% | 2275 |
| chr5 | 441419 | 0.24% | 2420 |
| chr6 | 492790 | 0.29% | 2645 |
| chr7 | 422022 | 0.26% | 2298 |
| chr8 | 370883 | 0.26% | 2035 |
| chr9 | 338119 | 0.24% | 1844 |
| chr10 | 368061 | 0.28% | 2029 |
| chr11 | 407314 | 0.30% | 2185 |
| chr12 | 412353 | 0.31% | 2238 |
| chr13 | 210824 | 0.18% | 1126 |
| chr14 | 259405 | 0.24% | 1342 |
| chr15 | 269492 | 0.26% | 1447 |
| chr16 | 242048 | 0.27% | 1348 |
| chr17 | 325536 | 0.39% | 1740 |
| chr18 | 177410 | 0.22% | 1001 |
| chr19 | 373926 | 0.64% | 1885 |
| chr20 | 199335 | 0.31% | 1108 |
| chr21 | 86144 | 0.18% | 484 |
| chr22 | 141381 | 0.28% | 766 |
| chrX | 186385 | 0.12% | 1046 |
| chrY | 7461 | 0.01% | 38 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 43715 | 1 | 1020 | 184.89 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF320BJH.bed.gz | 454.89 KB | f834232860f2deec79e7b24aac5d425e |
| ENCFF320BJH.tabix.bed.gz | 405.87 KB | 3e55d6cc369321246100880113e624bb |
| ENCFF320BJH.tabix.bed.gz.tbi | 253.1 KB | 4234a39bd2e8f7c41058b3005a8346bf |
| genomic_resource.yaml | 2.59 KB | 12a9ee2f0a9ea2bf174205c62eb06711 |
| statistics/ |