Resource
| Id | DNase-seq/ENCSR544KDB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR544KDB [biosample_summary="Homo sapiens thymus tissue male embryo (113 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (113 days) output_type: peaks audit_warning: Replicate 1_2 has no significant footprints detected. audit_warning: Alignment file {ENCFF166XSR|/files/ENCFF166XSR/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 38317259 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 {ENCFF166XSR|/files/ENCFF166XSR/} 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_ENCSR544KDB | float |
DNase-seq_ENCSR544KDB |
DNase-seq ENCSR544KDB [biosample_summary="Homo sapiens thymus tissue male embryo (113 days)"]
|
 |
[0.236, 14.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8408657 | 0.26% | 43245 |
| chr1 | 838080 | 0.34% | 4230 |
| chr2 | 636695 | 0.26% | 3297 |
| chr3 | 526582 | 0.27% | 2719 |
| chr4 | 380826 | 0.20% | 1956 |
| chr5 | 413638 | 0.23% | 2122 |
| chr6 | 522332 | 0.31% | 2621 |
| chr7 | 413951 | 0.26% | 2129 |
| chr8 | 342272 | 0.24% | 1796 |
| chr9 | 338790 | 0.24% | 1775 |
| chr10 | 398951 | 0.30% | 2053 |
| chr11 | 409902 | 0.30% | 2152 |
| chr12 | 440184 | 0.33% | 2222 |
| chr13 | 204651 | 0.18% | 1033 |
| chr14 | 279791 | 0.26% | 1419 |
| chr15 | 275315 | 0.27% | 1438 |
| chr16 | 291156 | 0.32% | 1501 |
| chr17 | 417825 | 0.50% | 2175 |
| chr18 | 161718 | 0.20% | 846 |
| chr19 | 438413 | 0.75% | 2185 |
| chr20 | 202233 | 0.31% | 1083 |
| chr21 | 96756 | 0.21% | 486 |
| chr22 | 168851 | 0.33% | 892 |
| chrX | 199252 | 0.13% | 1063 |
| chrY | 10493 | 0.02% | 52 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 43245 | 4 | 900 | 194.44 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF361OCI.bed.gz | 445.06 KB | 327a99837693429a903a58915b39ce53 |
| ENCFF361OCI.tabix.bed.gz | 406.75 KB | 77a70401896329cb2a3bc2ab7538e4e3 |
| ENCFF361OCI.tabix.bed.gz.tbi | 231.64 KB | 8cbc7016d573c37c2382f38201927cd8 |
| genomic_resource.yaml | 2.72 KB | 8894637819f986ded055578f323e1084 |
| statistics/ |