Resource
| Id | DNase-seq/ENCSR118WIQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR118WIQ [biosample_summary="Homo sapiens brain tissue embryo (112 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: embryo (112 days) output_type: peaks audit_warning: Alignment file {ENCFF802SKX|/files/ENCFF802SKX/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 34332656 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 {ENCFF802SKX|/files/ENCFF802SKX/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR118WIQ | float |
DNase-seq_ENCSR118WIQ |
DNase-seq ENCSR118WIQ [biosample_summary="Homo sapiens brain tissue embryo (112 days)"]
|
 |
[0.205, 10] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8519899 | 0.26% | 41622 |
| chr1 | 774232 | 0.31% | 3691 |
| chr2 | 671651 | 0.28% | 3310 |
| chr3 | 593261 | 0.30% | 2909 |
| chr4 | 452864 | 0.24% | 2265 |
| chr5 | 494165 | 0.27% | 2429 |
| chr6 | 547845 | 0.32% | 2630 |
| chr7 | 463466 | 0.29% | 2308 |
| chr8 | 386871 | 0.27% | 1907 |
| chr9 | 372066 | 0.27% | 1856 |
| chr10 | 363805 | 0.27% | 1834 |
| chr11 | 434163 | 0.32% | 2086 |
| chr12 | 436186 | 0.33% | 2089 |
| chr13 | 239873 | 0.21% | 1188 |
| chr14 | 311066 | 0.29% | 1458 |
| chr15 | 262527 | 0.26% | 1310 |
| chr16 | 259620 | 0.29% | 1301 |
| chr17 | 305660 | 0.37% | 1498 |
| chr18 | 181592 | 0.23% | 883 |
| chr19 | 345051 | 0.59% | 1544 |
| chr20 | 192871 | 0.30% | 989 |
| chr21 | 89070 | 0.19% | 446 |
| chr22 | 118335 | 0.23% | 583 |
| chrX | 223519 | 0.14% | 1107 |
| chrY | 140 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41622 | 1 | 1100 | 204.7 | 188 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF546VAB.bed.gz | 423.86 KB | b5ddce5c8fef23104a255c50ba1de3de |
| ENCFF546VAB.tabix.bed.gz | 384.85 KB | 2d7b02a6dc06b7e227b3d99243250e11 |
| ENCFF546VAB.tabix.bed.gz.tbi | 230.25 KB | d1fc90f37bcec57da5a0b55806b0775a |
| genomic_resource.yaml | 2.61 KB | 734b9c390f79638e410cbce16f72d3a2 |
| statistics/ |