Resource
| Id | DNase-seq/ENCSR536NGW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR536NGW [biosample_summary="Homo sapiens heart tissue male embryo (96 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (96 days) output_type: peaks audit_warning: Replicate 1_3 has no significant footprints detected. audit_warning: Alignment file {ENCFF495CNT|/files/ENCFF495CNT/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 24963696 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 {ENCFF495CNT|/files/ENCFF495CNT/} 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_ENCSR536NGW | float |
DNase-seq_ENCSR536NGW |
DNase-seq ENCSR536NGW [biosample_summary="Homo sapiens heart tissue male embryo (96 days)"]
|
 |
[0.373, 10.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 3430396 | 0.11% | 18073 |
| chr1 | 343543 | 0.14% | 1773 |
| chr2 | 270408 | 0.11% | 1467 |
| chr3 | 227437 | 0.11% | 1181 |
| chr4 | 186383 | 0.10% | 948 |
| chr5 | 184649 | 0.10% | 1008 |
| chr6 | 203671 | 0.12% | 1096 |
| chr7 | 179982 | 0.11% | 937 |
| chr8 | 131355 | 0.09% | 704 |
| chr9 | 140533 | 0.10% | 754 |
| chr10 | 149727 | 0.11% | 801 |
| chr11 | 175727 | 0.13% | 927 |
| chr12 | 181050 | 0.14% | 943 |
| chr13 | 83661 | 0.07% | 447 |
| chr14 | 113111 | 0.11% | 573 |
| chr15 | 116345 | 0.11% | 606 |
| chr16 | 108825 | 0.12% | 584 |
| chr17 | 147553 | 0.18% | 765 |
| chr18 | 67618 | 0.08% | 364 |
| chr19 | 211209 | 0.36% | 1030 |
| chr20 | 71324 | 0.11% | 385 |
| chr21 | 30566 | 0.07% | 171 |
| chr22 | 51157 | 0.10% | 280 |
| chrX | 51249 | 0.03% | 310 |
| chrY | 3313 | 0.01% | 19 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 18073 | 5 | 980 | 189.81 | 173 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF227DNW.bed.gz | 179.54 KB | 4b785ea051c340d3100ef231f93b51da |
| ENCFF227DNW.tabix.bed.gz | 163.46 KB | 0b3592e142dff00d8425fcd8dde2c8b5 |
| ENCFF227DNW.tabix.bed.gz.tbi | 100.42 KB | 17fa49f6babdba65a967977c3dd0a5cb |
| genomic_resource.yaml | 2.71 KB | 3055905c6bf8ed92aa5cfadbe50de0fe |
| statistics/ |