Resource
| Id | DNase-seq/ENCSR662HMO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR662HMO [biosample_summary="Homo sapiens NAMALWA"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: peaks 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 {ENCFF461HFP|/files/ENCFF461HFP/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.40. 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: 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 {ENCFF628MNE|/files/ENCFF628MNE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.29. 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_ENCSR662HMO | float |
DNase-seq_ENCSR662HMO |
DNase-seq ENCSR662HMO [biosample_summary="Homo sapiens NAMALWA"]
|
 |
[0.0231, 36.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 28833113 | 0.90% | 135974 |
| chr1 | 2786479 | 1.12% | 12919 |
| chr2 | 2250200 | 0.93% | 10635 |
| chr3 | 1786244 | 0.90% | 8426 |
| chr4 | 1348965 | 0.71% | 6471 |
| chr5 | 1515415 | 0.83% | 7150 |
| chr6 | 1765547 | 1.03% | 8138 |
| chr7 | 1607693 | 1.01% | 7581 |
| chr8 | 1112257 | 0.77% | 5316 |
| chr9 | 1159963 | 0.84% | 5503 |
| chr10 | 1244863 | 0.93% | 5923 |
| chr11 | 1299384 | 0.96% | 6214 |
| chr12 | 1554995 | 1.17% | 7161 |
| chr13 | 807957 | 0.71% | 3763 |
| chr14 | 863242 | 0.81% | 4135 |
| chr15 | 893024 | 0.88% | 4256 |
| chr16 | 1078066 | 1.19% | 5078 |
| chr17 | 1278806 | 1.54% | 5999 |
| chr18 | 591578 | 0.74% | 2849 |
| chr19 | 1274231 | 2.17% | 5918 |
| chr20 | 768411 | 1.19% | 3696 |
| chr21 | 341931 | 0.73% | 1618 |
| chr22 | 640248 | 1.26% | 2992 |
| chrX | 862334 | 0.55% | 4223 |
| chrY | 1280 | <0.01% | 10 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 135974 | 1 | 1060 | 212.05 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF718RMW.bed.gz | 1.47 MB | d153142cf2504d06ec1ba6121318d812 |
| ENCFF718RMW.tabix.bed.gz | 1.36 MB | bab7c1144fbe66e07fb9d6bbf6260c48 |
| ENCFF718RMW.tabix.bed.gz.tbi | 479.99 KB | a9d2d99eeee362f5a9bc1ae8610de46b |
| genomic_resource.yaml | 2.77 KB | 048828a91bfaea9e27db173f5637449f |
| statistics/ |