Resource
| Id | DNase-seq/ENCSR627UDJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR627UDJ [biosample_summary="Homo sapiens T-cell male adult (36 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (36 years) output_type: peaks audit_error: 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 {ENCFF838LVF|/files/ENCFF838LVF/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.24. 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/}) audit_warning: Alignment file {ENCFF838LVF|/files/ENCFF838LVF/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 32234237 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR627UDJ | float |
DNase-seq_ENCSR627UDJ |
DNase-seq ENCSR627UDJ [biosample_summary="Homo sapiens T-cell male adult (36 years)"]
|
 |
[0.281, 79.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5151936 | 0.16% | 28254 |
| chr1 | 526319 | 0.21% | 2897 |
| chr2 | 381478 | 0.16% | 2095 |
| chr3 | 306607 | 0.15% | 1685 |
| chr4 | 203813 | 0.11% | 1138 |
| chr5 | 249829 | 0.14% | 1376 |
| chr6 | 344350 | 0.20% | 1876 |
| chr7 | 235881 | 0.15% | 1292 |
| chr8 | 184376 | 0.13% | 1053 |
| chr9 | 188975 | 0.14% | 1054 |
| chr10 | 224118 | 0.17% | 1244 |
| chr11 | 248397 | 0.18% | 1363 |
| chr12 | 288380 | 0.22% | 1577 |
| chr13 | 121830 | 0.11% | 667 |
| chr14 | 177025 | 0.17% | 972 |
| chr15 | 160345 | 0.16% | 878 |
| chr16 | 182633 | 0.20% | 1004 |
| chr17 | 273701 | 0.33% | 1502 |
| chr18 | 83082 | 0.10% | 465 |
| chr19 | 315073 | 0.54% | 1629 |
| chr20 | 123580 | 0.19% | 689 |
| chr21 | 62092 | 0.13% | 332 |
| chr22 | 105412 | 0.21% | 579 |
| chrX | 164358 | 0.11% | 885 |
| chrY | 282 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 28254 | 2 | 640 | 182.34 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF331AUI.bed.gz | 305.58 KB | ce13fce941455ce81b128bd843a410fa |
| ENCFF331AUI.tabix.bed.gz | 275.7 KB | 4ce7ac9125de42a1bb4f95ff14ce0005 |
| ENCFF331AUI.tabix.bed.gz.tbi | 169.18 KB | 81287b70b0b130c4e60bc50346772f9d |
| genomic_resource.yaml | 2.62 KB | 8aa85cecfc586510878db19804433981 |
| statistics/ |