Resource
| Id | DNase-seq/ENCSR346JWH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR346JWH [biosample_summary="Homo sapiens A673"] |
| 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 {ENCFF261YSH|/files/ENCFF261YSH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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 {ENCFF860UCH|/files/ENCFF860UCH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.36. 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_ENCSR346JWH | float |
DNase-seq_ENCSR346JWH |
DNase-seq ENCSR346JWH [biosample_summary="Homo sapiens A673"]
|
 |
[0.0334, 30.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 35660878 | 1.11% | 181556 |
| chr1 | 3229295 | 1.30% | 16311 |
| chr2 | 2973026 | 1.23% | 15186 |
| chr3 | 2301305 | 1.16% | 11739 |
| chr4 | 1960772 | 1.03% | 10037 |
| chr5 | 1925190 | 1.06% | 9859 |
| chr6 | 2330214 | 1.36% | 11690 |
| chr7 | 1789710 | 1.12% | 9234 |
| chr8 | 1790430 | 1.23% | 9082 |
| chr9 | 1363686 | 0.99% | 6960 |
| chr10 | 1675700 | 1.25% | 8529 |
| chr11 | 1931218 | 1.43% | 9773 |
| chr12 | 1860950 | 1.40% | 9428 |
| chr13 | 1130823 | 0.99% | 5713 |
| chr14 | 1224201 | 1.14% | 6217 |
| chr15 | 1053403 | 1.03% | 5394 |
| chr16 | 1058198 | 1.17% | 5439 |
| chr17 | 1253457 | 1.51% | 6384 |
| chr18 | 816824 | 1.02% | 4167 |
| chr19 | 1117351 | 1.91% | 5536 |
| chr20 | 857321 | 1.33% | 4436 |
| chr21 | 359106 | 0.77% | 1861 |
| chr22 | 553089 | 1.09% | 2857 |
| chrX | 1103826 | 0.71% | 5710 |
| chrY | 1783 | <0.01% | 14 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 181556 | 1 | 920 | 196.42 | 192 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF355NVJ.bed.gz | 1.95 MB | 0c2a155608167660072385c5452e0224 |
| ENCFF355NVJ.tabix.bed.gz | 1.78 MB | 07903c3078b7f9fbbbe9a59b926a36d9 |
| ENCFF355NVJ.tabix.bed.gz.tbi | 632.97 KB | a6e97cdb6f26013ca2593e692c1877ce |
| genomic_resource.yaml | 2.76 KB | 74d7ee3d77021876401563ae8eaae3d2 |
| statistics/ |