Resource
| Id | DNase-seq/ENCSR000EJJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EJJ [biosample_summary="Homo sapiens GM19238"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: peaks audit_internal_action: Released analysis {ENCAN229RLD|/analyses/ENCAN229RLD/} has in progress subobject document {38444c70-5666-40d2-af67-8eed484d4b8c|/documents/38444c70-5666-40d2-af67-8eed484d4b8c/} 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 {ENCFF153GQF|/files/ENCFF153GQF/} processed by DNase-seq ENCODE4 v3.0.0 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_ENCSR000EJJ | float |
DNase-seq_ENCSR000EJJ |
DNase-seq ENCSR000EJJ [biosample_summary="Homo sapiens GM19238"]
|
 |
[0.15, 27] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9588160 | 0.30% | 53735 |
| chr1 | 936786 | 0.38% | 5246 |
| chr2 | 667856 | 0.28% | 3762 |
| chr3 | 550201 | 0.28% | 3087 |
| chr4 | 368854 | 0.19% | 2104 |
| chr5 | 453504 | 0.25% | 2571 |
| chr6 | 543339 | 0.32% | 3105 |
| chr7 | 433004 | 0.27% | 2455 |
| chr8 | 381019 | 0.26% | 2174 |
| chr9 | 406622 | 0.29% | 2288 |
| chr10 | 431576 | 0.32% | 2451 |
| chr11 | 516851 | 0.38% | 2849 |
| chr12 | 492127 | 0.37% | 2789 |
| chr13 | 194991 | 0.17% | 1102 |
| chr14 | 321373 | 0.30% | 1788 |
| chr15 | 318018 | 0.31% | 1793 |
| chr16 | 405570 | 0.45% | 2204 |
| chr17 | 557172 | 0.67% | 3101 |
| chr18 | 174977 | 0.22% | 1000 |
| chr19 | 587136 | 1.00% | 3087 |
| chr20 | 269953 | 0.42% | 1517 |
| chr21 | 101149 | 0.22% | 574 |
| chr22 | 235900 | 0.46% | 1305 |
| chrX | 240182 | 0.15% | 1383 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 53735 | 3 | 720 | 178.43 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF013CYL.bed.gz | 578.77 KB | 2d2caf1ff05a74aaf3696511c25907af |
| ENCFF013CYL.tabix.bed.gz | 524.46 KB | 5cf2ceb7b278985b7ae80b351f2a02cd |
| ENCFF013CYL.tabix.bed.gz.tbi | 259.08 KB | 40c6d1ea29c1a81c385d93874be8e968 |
| genomic_resource.yaml | 2.13 KB | 8f6a0a9f535847fea6ae192fb08b30b4 |
| statistics/ |