Resource
| Id | DNase-seq/ENCSR000ENV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000ENV [biosample_summary="Homo sapiens mammary epithelial cell female"] |
| Description |
status: released biological_replicates: Rep 1 summary: female output_type: peaks audit_warning: Alignment file {ENCFF619RSR|/files/ENCFF619RSR/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 30795569 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: Alignment file {ENCFF698JTA|/files/ENCFF698JTA/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 23997781 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 {ENCFF619RSR|/files/ENCFF619RSR/} 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000ENV | float |
DNase-seq_ENCSR000ENV |
DNase-seq ENCSR000ENV [biosample_summary="Homo sapiens mammary epithelial cell female"]
|
 |
[0.264, 39.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12433825 | 0.39% | 71395 |
| chr1 | 1159633 | 0.47% | 6643 |
| chr2 | 1007549 | 0.42% | 5888 |
| chr3 | 844624 | 0.43% | 4852 |
| chr4 | 679523 | 0.36% | 3987 |
| chr5 | 712980 | 0.39% | 4154 |
| chr6 | 790052 | 0.46% | 4548 |
| chr7 | 645466 | 0.41% | 3721 |
| chr8 | 583537 | 0.40% | 3401 |
| chr9 | 516640 | 0.37% | 2969 |
| chr10 | 573672 | 0.43% | 3304 |
| chr11 | 632269 | 0.47% | 3636 |
| chr12 | 643964 | 0.48% | 3683 |
| chr13 | 349660 | 0.31% | 2009 |
| chr14 | 378151 | 0.35% | 2174 |
| chr15 | 382391 | 0.37% | 2195 |
| chr16 | 368946 | 0.41% | 2075 |
| chr17 | 491390 | 0.59% | 2710 |
| chr18 | 300989 | 0.37% | 1751 |
| chr19 | 412818 | 0.70% | 2145 |
| chr20 | 302666 | 0.47% | 1748 |
| chr21 | 137141 | 0.29% | 788 |
| chr22 | 190982 | 0.38% | 1062 |
| chrX | 328191 | 0.21% | 1947 |
| chrY | 591 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 71395 | 4 | 860 | 174.16 | 160 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF628QME.bed.gz | 746.73 KB | 277779ba44ec6253596a33d581d34d24 |
| ENCFF628QME.tabix.bed.gz | 673.2 KB | 4320a8d98fec7dfa6bb6271917667f5b |
| ENCFF628QME.tabix.bed.gz.tbi | 368.11 KB | 34180c73d19c356ba27a5cd806cd5015 |
| genomic_resource.yaml | 3.21 KB | 6bb550396dee4aecf5e0dc3fb62186fe |
| statistics/ |