Resource
| Id | DNase-seq/ENCSR926SNI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR926SNI [biosample_summary="Homo sapiens T-cell male adult (38 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (38 years) output_type: peaks audit_warning: Alignment file {ENCFF252DLW|/files/ENCFF252DLW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 29004262 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 {ENCFF252DLW|/files/ENCFF252DLW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.35. 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_ENCSR926SNI | float |
DNase-seq_ENCSR926SNI |
DNase-seq ENCSR926SNI [biosample_summary="Homo sapiens T-cell male adult (38 years)"]
|
 |
[0.45, 32] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4955585 | 0.15% | 26213 |
| chr1 | 510847 | 0.21% | 2697 |
| chr2 | 331428 | 0.14% | 1745 |
| chr3 | 267646 | 0.13% | 1413 |
| chr4 | 164076 | 0.09% | 873 |
| chr5 | 215665 | 0.12% | 1147 |
| chr6 | 271734 | 0.16% | 1447 |
| chr7 | 225669 | 0.14% | 1209 |
| chr8 | 173936 | 0.12% | 947 |
| chr9 | 193220 | 0.14% | 1017 |
| chr10 | 208775 | 0.16% | 1106 |
| chr11 | 265693 | 0.20% | 1411 |
| chr12 | 258411 | 0.19% | 1353 |
| chr13 | 98122 | 0.09% | 514 |
| chr14 | 173354 | 0.16% | 924 |
| chr15 | 160878 | 0.16% | 872 |
| chr16 | 218529 | 0.24% | 1134 |
| chr17 | 311110 | 0.37% | 1662 |
| chr18 | 69669 | 0.09% | 379 |
| chr19 | 382114 | 0.65% | 1944 |
| chr20 | 137511 | 0.21% | 730 |
| chr21 | 54867 | 0.12% | 300 |
| chr22 | 127625 | 0.25% | 678 |
| chrX | 128783 | 0.08% | 683 |
| chrY | 5923 | 0.01% | 28 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 26213 | 12 | 720 | 189.05 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF436SLI.bed.gz | 285.57 KB | 269024531672a4e9986cfe04bee5ee13 |
| ENCFF436SLI.tabix.bed.gz | 258.01 KB | 5fab6729c5a2b7e45d3d85417564e274 |
| ENCFF436SLI.tabix.bed.gz.tbi | 160.47 KB | 7c5816faff9ead9c04d27b5ae4680eed |
| genomic_resource.yaml | 2.62 KB | fed2945222aec01f34794d02e8552c86 |
| statistics/ |