Resource
| Id | DNase-seq/ENCSR154YPL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR154YPL [biosample_summary="Homo sapiens large intestine tissue female embryo (110 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (110 days) output_type: peaks audit_warning: Alignment file {ENCFF649HNY|/files/ENCFF649HNY/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 35991094 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 {ENCFF649HNY|/files/ENCFF649HNY/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) 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-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR154YPL | float |
DNase-seq_ENCSR154YPL |
DNase-seq ENCSR154YPL [biosample_summary="Homo sapiens large intestine tissue female embryo (110 days)"]
|
 |
[0.223, 17.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10080357 | 0.31% | 53327 |
| chr1 | 941168 | 0.38% | 4985 |
| chr2 | 804766 | 0.33% | 4284 |
| chr3 | 666810 | 0.34% | 3526 |
| chr4 | 525060 | 0.28% | 2826 |
| chr5 | 538079 | 0.30% | 2878 |
| chr6 | 626300 | 0.37% | 3294 |
| chr7 | 511240 | 0.32% | 2722 |
| chr8 | 444758 | 0.31% | 2365 |
| chr9 | 429884 | 0.31% | 2284 |
| chr10 | 453564 | 0.34% | 2414 |
| chr11 | 527170 | 0.39% | 2787 |
| chr12 | 523088 | 0.39% | 2748 |
| chr13 | 250696 | 0.22% | 1337 |
| chr14 | 341897 | 0.32% | 1778 |
| chr15 | 304016 | 0.30% | 1622 |
| chr16 | 322699 | 0.36% | 1725 |
| chr17 | 420408 | 0.50% | 2197 |
| chr18 | 228896 | 0.28% | 1186 |
| chr19 | 416636 | 0.71% | 2031 |
| chr20 | 244972 | 0.38% | 1309 |
| chr21 | 111561 | 0.24% | 593 |
| chr22 | 178438 | 0.35% | 977 |
| chrX | 267849 | 0.17% | 1456 |
| chrY | 402 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 53327 | 3 | 840 | 189.03 | 183 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF486QCQ.bed.gz | 564.15 KB | 4e4c224efc1e30faff82ea8ebb61ce95 |
| ENCFF486QCQ.tabix.bed.gz | 503.03 KB | a2573eed977c79b6e9165688d33f4882 |
| ENCFF486QCQ.tabix.bed.gz.tbi | 293.43 KB | 17cdd094d5dd80972edc1daf889884f4 |
| genomic_resource.yaml | 2.68 KB | bdd4dddd9bb8edd2f8879789509b4152 |
| statistics/ |