Resource
| Id | DNase-seq/ENCSR718AAB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR718AAB [biosample_summary="Homo sapiens natural killer cell male adult (37 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (37 years) output_type: peaks audit_error: 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 {ENCFF118JHP|/files/ENCFF118JHP/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.25. 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/}) audit_internal_action: Archived analysis {ENCAN200GPV|/analyses/ENCAN200GPV/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF808HRA|/files/ENCFF808HRA/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 28814796 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/}) audit_warning: Alignment file {ENCFF118JHP|/files/ENCFF118JHP/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 28568251 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR718AAB | float |
DNase-seq_ENCSR718AAB |
DNase-seq ENCSR718AAB [biosample_summary="Homo sapiens natural killer cell male adult (37 years)"]
|
 |
[4, 895] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6329975 | 0.20% | 42118 |
| chr1 | 641772 | 0.26% | 4274 |
| chr2 | 470111 | 0.19% | 3124 |
| chr3 | 365975 | 0.18% | 2433 |
| chr4 | 240300 | 0.13% | 1597 |
| chr5 | 302550 | 0.17% | 2012 |
| chr6 | 382771 | 0.22% | 2549 |
| chr7 | 302862 | 0.19% | 2015 |
| chr8 | 246065 | 0.17% | 1636 |
| chr9 | 259170 | 0.19% | 1725 |
| chr10 | 293131 | 0.22% | 1949 |
| chr11 | 324383 | 0.24% | 2158 |
| chr12 | 321102 | 0.24% | 2139 |
| chr13 | 146506 | 0.13% | 976 |
| chr14 | 212722 | 0.20% | 1418 |
| chr15 | 212550 | 0.21% | 1412 |
| chr16 | 244440 | 0.27% | 1627 |
| chr17 | 343958 | 0.41% | 2290 |
| chr18 | 105875 | 0.13% | 702 |
| chr19 | 354983 | 0.61% | 2366 |
| chr20 | 169500 | 0.26% | 1126 |
| chr21 | 69750 | 0.15% | 464 |
| chr22 | 141749 | 0.28% | 943 |
| chrX | 168450 | 0.11% | 1121 |
| chrY | 9300 | 0.02% | 62 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 42118 | 32 | 450 | 150.29 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF770IDH.bed.gz | 412.28 KB | 8392d10a91cf983e297dc7d492b579e5 |
| ENCFF770IDH.tabix.bed.gz | 355.54 KB | 0138c5b25fb1f56ba29f66765d40df80 |
| ENCFF770IDH.tabix.bed.gz.tbi | 235.41 KB | c12fe3f2691645bae0dbe1418b3d719f |
| genomic_resource.yaml | 3.39 KB | 946197c637472586132d7c6be0a20ede |
| statistics/ |