Resource
| Id | DNase-seq/ENCSR679IFH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR679IFH [biosample_summary="Homo sapiens spleen tissue embryo (112 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: embryo (112 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN893QMM|/analyses/ENCAN893QMM/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF898APF|/files/ENCFF898APF/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 28411299 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 {ENCFF701NOD|/files/ENCFF701NOD/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 28196873 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 {ENCFF701NOD|/files/ENCFF701NOD/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.35. 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_ENCSR679IFH | float |
DNase-seq_ENCSR679IFH |
DNase-seq ENCSR679IFH [biosample_summary="Homo sapiens spleen tissue embryo (112 days)"]
|
 |
[3, 1.64e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10214571 | 0.32% | 67864 |
| chr1 | 967339 | 0.39% | 6427 |
| chr2 | 838730 | 0.35% | 5564 |
| chr3 | 692107 | 0.35% | 4603 |
| chr4 | 534216 | 0.28% | 3550 |
| chr5 | 568413 | 0.31% | 3774 |
| chr6 | 627789 | 0.37% | 4173 |
| chr7 | 522630 | 0.33% | 3467 |
| chr8 | 454636 | 0.31% | 3022 |
| chr9 | 404089 | 0.29% | 2691 |
| chr10 | 502299 | 0.38% | 3340 |
| chr11 | 507197 | 0.38% | 3368 |
| chr12 | 516383 | 0.39% | 3431 |
| chr13 | 286820 | 0.25% | 1901 |
| chr14 | 331469 | 0.31% | 2201 |
| chr15 | 315832 | 0.31% | 2096 |
| chr16 | 309093 | 0.34% | 2057 |
| chr17 | 414575 | 0.50% | 2757 |
| chr18 | 227659 | 0.28% | 1510 |
| chr19 | 365517 | 0.62% | 2428 |
| chr20 | 247800 | 0.38% | 1647 |
| chr21 | 116365 | 0.25% | 773 |
| chr22 | 174150 | 0.34% | 1159 |
| chrX | 288713 | 0.19% | 1920 |
| chrY | 750 | <0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 67864 | 2 | 532 | 150.52 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF376YIY.bed.gz | 661.1 KB | adc8b41a68ad1d4948bad23a186ef132 |
| ENCFF376YIY.tabix.bed.gz | 565.13 KB | 89e431f2c83dc6a0aeda77f54b24047e |
| ENCFF376YIY.tabix.bed.gz.tbi | 369.95 KB | bb2094512054b361307d81688dd0b23d |
| genomic_resource.yaml | 3.35 KB | 516c83bdc299dc014385000c65820ef7 |
| statistics/ |