Resource
| Id | DNase-seq/ENCSR262QJC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR262QJC [biosample_summary="Homo sapiens kidney tissue male embryo (87 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (87 days) output_type: peaks audit_warning: Alignment file {ENCFF126PCH|/files/ENCFF126PCH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 24316994 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 {ENCFF126PCH|/files/ENCFF126PCH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.26. 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_ENCSR262QJC | float |
DNase-seq_ENCSR262QJC |
DNase-seq ENCSR262QJC [biosample_summary="Homo sapiens kidney tissue male embryo (87 days)"]
|
 |
[0.33, 27.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4093710 | 0.13% | 23422 |
| chr1 | 399939 | 0.16% | 2206 |
| chr2 | 317522 | 0.13% | 1821 |
| chr3 | 272286 | 0.14% | 1556 |
| chr4 | 209827 | 0.11% | 1219 |
| chr5 | 228743 | 0.13% | 1302 |
| chr6 | 245548 | 0.14% | 1391 |
| chr7 | 208282 | 0.13% | 1209 |
| chr8 | 175558 | 0.12% | 1024 |
| chr9 | 159215 | 0.12% | 926 |
| chr10 | 182521 | 0.14% | 1066 |
| chr11 | 215965 | 0.16% | 1226 |
| chr12 | 222798 | 0.17% | 1250 |
| chr13 | 95877 | 0.08% | 547 |
| chr14 | 143798 | 0.13% | 812 |
| chr15 | 130002 | 0.13% | 744 |
| chr16 | 125590 | 0.14% | 754 |
| chr17 | 167474 | 0.20% | 975 |
| chr18 | 85142 | 0.11% | 492 |
| chr19 | 217283 | 0.37% | 1139 |
| chr20 | 105055 | 0.16% | 639 |
| chr21 | 41170 | 0.09% | 251 |
| chr22 | 64121 | 0.13% | 383 |
| chrX | 77251 | 0.05% | 471 |
| chrY | 2743 | <0.01% | 19 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 23422 | 4 | 900 | 174.78 | 160 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF720ENQ.bed.gz | 240.89 KB | 1c745ce892406dccef29f42524f87f7f |
| ENCFF720ENQ.tabix.bed.gz | 214.7 KB | 8ede99a39bf31f6e1ff7a801bfaaed7c |
| ENCFF720ENQ.tabix.bed.gz.tbi | 156.7 KB | 0b88f3a190c8cb66b238a33868cfa2be |
| genomic_resource.yaml | 2.64 KB | c91ff553fdb7a22fbe58f2a9798d0c6a |
| statistics/ |