Resource
| Id | DNase-seq/ENCSR856QJX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR856QJX [biosample_summary="Homo sapiens adrenal gland tissue male embryo (85 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (85 days) output_type: peaks audit_warning: Alignment file {ENCFF022KTP|/files/ENCFF022KTP/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 32314013 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 {ENCFF022KTP|/files/ENCFF022KTP/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.31. 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_ENCSR856QJX | float |
DNase-seq_ENCSR856QJX |
DNase-seq ENCSR856QJX [biosample_summary="Homo sapiens adrenal gland tissue male embryo (85 days)"]
|
 |
[0.248, 10.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7454383 | 0.23% | 41006 |
| chr1 | 698840 | 0.28% | 3763 |
| chr2 | 567797 | 0.23% | 3151 |
| chr3 | 474701 | 0.24% | 2629 |
| chr4 | 376024 | 0.20% | 2060 |
| chr5 | 416349 | 0.23% | 2315 |
| chr6 | 441093 | 0.26% | 2428 |
| chr7 | 384470 | 0.24% | 2151 |
| chr8 | 317704 | 0.22% | 1781 |
| chr9 | 302156 | 0.22% | 1667 |
| chr10 | 335654 | 0.25% | 1878 |
| chr11 | 385794 | 0.29% | 2082 |
| chr12 | 379619 | 0.28% | 2084 |
| chr13 | 187659 | 0.16% | 1063 |
| chr14 | 249791 | 0.23% | 1338 |
| chr15 | 248839 | 0.24% | 1380 |
| chr16 | 244082 | 0.27% | 1344 |
| chr17 | 313008 | 0.38% | 1723 |
| chr18 | 154090 | 0.19% | 874 |
| chr19 | 377404 | 0.64% | 1879 |
| chr20 | 188111 | 0.29% | 1095 |
| chr21 | 81688 | 0.17% | 478 |
| chr22 | 139895 | 0.28% | 775 |
| chrX | 173070 | 0.11% | 979 |
| chrY | 16545 | 0.03% | 89 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41006 | 2 | 820 | 181.79 | 175 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF744JJO.bed.gz | 428.0 KB | 8f488c5e079aa057cddecc756c7662db |
| ENCFF744JJO.tabix.bed.gz | 382.21 KB | 56e6198fbee3e0a0cf1567ad2be5c2fa |
| ENCFF744JJO.tabix.bed.gz.tbi | 244.44 KB | 6786124a5f920497087de3ff9087ffd0 |
| genomic_resource.yaml | 2.66 KB | 45ec4565e06319b40b6b1743773910a7 |
| statistics/ |