Resource
| Id | DNase-seq/ENCSR000ENM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000ENM [biosample_summary="Homo sapiens HCT116"] |
| Description |
status: released biological_replicates: Rep 2 summary: output_type: peaks audit_warning: Alignment file {ENCFF969VWM|/files/ENCFF969VWM/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 26087726 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 {ENCFF304MDQ|/files/ENCFF304MDQ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 30888113 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 {ENCFF304MDQ|/files/ENCFF304MDQ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.39. 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_ENCSR000ENM | float |
DNase-seq_ENCSR000ENM |
DNase-seq ENCSR000ENM [biosample_summary="Homo sapiens HCT116"]
|
 |
[0.228, 48.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12016115 | 0.37% | 67708 |
| chr1 | 1136374 | 0.46% | 6416 |
| chr2 | 925887 | 0.38% | 5256 |
| chr3 | 761079 | 0.38% | 4317 |
| chr4 | 621244 | 0.33% | 3548 |
| chr5 | 629144 | 0.35% | 3563 |
| chr6 | 757671 | 0.44% | 4243 |
| chr7 | 614029 | 0.39% | 3494 |
| chr8 | 564295 | 0.39% | 3185 |
| chr9 | 471022 | 0.34% | 2671 |
| chr10 | 590544 | 0.44% | 3332 |
| chr11 | 597111 | 0.44% | 3364 |
| chr12 | 635217 | 0.48% | 3586 |
| chr13 | 264669 | 0.23% | 1512 |
| chr14 | 373830 | 0.35% | 2104 |
| chr15 | 365744 | 0.36% | 2093 |
| chr16 | 406640 | 0.45% | 2291 |
| chr17 | 592918 | 0.71% | 3260 |
| chr18 | 224142 | 0.28% | 1274 |
| chr19 | 521432 | 0.89% | 2764 |
| chr20 | 309781 | 0.48% | 1776 |
| chr21 | 105887 | 0.23% | 587 |
| chr22 | 219852 | 0.43% | 1243 |
| chrX | 323364 | 0.21% | 1803 |
| chrY | 4239 | 0.01% | 26 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 67708 | 3 | 720 | 177.47 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF240LRP.bed.gz | 715.99 KB | 7ac7c1d3717ec5ead65b83847be4c8b0 |
| ENCFF240LRP.tabix.bed.gz | 644.26 KB | 80d7af703bcf28d4fef9543bbc5a01cb |
| ENCFF240LRP.tabix.bed.gz.tbi | 353.32 KB | a545671897cde07b04ae178816ea2df4 |
| genomic_resource.yaml | 3.2 KB | 6c2237715a7cfc2a86eae3d31c65c7a7 |
| statistics/ |