Resource
| Id | DNase-seq/ENCSR723JLG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR723JLG [biosample_summary="Homo sapiens natural killer cell female adult (34 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (34 years) output_type: peaks audit_internal_action: Archived analysis {ENCAN805CWU|/analyses/ENCAN805CWU/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF559IYX|/files/ENCFF559IYX/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 34817481 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 {ENCFF368ONB|/files/ENCFF368ONB/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 34533807 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: 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 {ENCFF368ONB|/files/ENCFF368ONB/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.31. 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR723JLG | float |
DNase-seq_ENCSR723JLG |
DNase-seq ENCSR723JLG [biosample_summary="Homo sapiens natural killer cell female adult (34 years)"]
|
 |
[5, 792] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8555501 | 0.27% | 56808 |
| chr1 | 826695 | 0.33% | 5491 |
| chr2 | 684067 | 0.28% | 4531 |
| chr3 | 526748 | 0.27% | 3493 |
| chr4 | 387075 | 0.20% | 2562 |
| chr5 | 440632 | 0.24% | 2927 |
| chr6 | 534214 | 0.31% | 3548 |
| chr7 | 408191 | 0.26% | 2712 |
| chr8 | 357659 | 0.25% | 2379 |
| chr9 | 347539 | 0.25% | 2305 |
| chr10 | 406618 | 0.30% | 2701 |
| chr11 | 425526 | 0.32% | 2834 |
| chr12 | 447014 | 0.34% | 2962 |
| chr13 | 215480 | 0.19% | 1432 |
| chr14 | 288178 | 0.27% | 1916 |
| chr15 | 273259 | 0.27% | 1814 |
| chr16 | 300276 | 0.33% | 1996 |
| chr17 | 408939 | 0.49% | 2718 |
| chr18 | 151901 | 0.19% | 1004 |
| chr19 | 375652 | 0.64% | 2499 |
| chr20 | 218193 | 0.34% | 1450 |
| chr21 | 91307 | 0.20% | 606 |
| chr22 | 166161 | 0.33% | 1109 |
| chrX | 273427 | 0.18% | 1814 |
| chrY | 750 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 56808 | 17 | 450 | 150.6 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF897BWP.bed.gz | 549.16 KB | efae57192b49622ad76bd3728ad6c18e |
| ENCFF897BWP.tabix.bed.gz | 472.5 KB | ecd1cbdb9d95772003faff0f8c89fb5f |
| ENCFF897BWP.tabix.bed.gz.tbi | 273.92 KB | c5ff45001c55e11254a3a4e286b6dbd2 |
| genomic_resource.yaml | 3.4 KB | db758d50734d80bf23ac0ec9b5ea5951 |
| statistics/ |