Resource
| Id | DNase-seq/ENCSR666YVE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR666YVE [biosample_summary="Homo sapiens large intestine tissue male embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (105 days) output_type: peaks audit_warning: Alignment file {ENCFF508JHO|/files/ENCFF508JHO/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 34978678 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 {ENCFF508JHO|/files/ENCFF508JHO/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.27. 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_ENCSR666YVE | float |
DNase-seq_ENCSR666YVE |
DNase-seq ENCSR666YVE [biosample_summary="Homo sapiens large intestine tissue male embryo (105 days)"]
|
 |
[0.23, 11.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5671673 | 0.18% | 28884 |
| chr1 | 533158 | 0.21% | 2632 |
| chr2 | 461357 | 0.19% | 2380 |
| chr3 | 382519 | 0.19% | 1952 |
| chr4 | 305111 | 0.16% | 1574 |
| chr5 | 300093 | 0.17% | 1517 |
| chr6 | 367686 | 0.22% | 1868 |
| chr7 | 301846 | 0.19% | 1554 |
| chr8 | 225861 | 0.16% | 1175 |
| chr9 | 223244 | 0.16% | 1162 |
| chr10 | 246283 | 0.18% | 1301 |
| chr11 | 291157 | 0.22% | 1478 |
| chr12 | 317488 | 0.24% | 1582 |
| chr13 | 157003 | 0.14% | 786 |
| chr14 | 196541 | 0.18% | 985 |
| chr15 | 185588 | 0.18% | 933 |
| chr16 | 167413 | 0.19% | 860 |
| chr17 | 226864 | 0.27% | 1171 |
| chr18 | 124322 | 0.15% | 646 |
| chr19 | 277671 | 0.47% | 1285 |
| chr20 | 125095 | 0.19% | 678 |
| chr21 | 53264 | 0.11% | 279 |
| chr22 | 81857 | 0.16% | 436 |
| chrX | 113621 | 0.07% | 613 |
| chrY | 6631 | 0.01% | 37 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 28884 | 1 | 1187 | 196.36 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF082MXZ.bed.gz | 290.71 KB | 169d0ef696376c6cfb44ae16838582c3 |
| ENCFF082MXZ.tabix.bed.gz | 264.55 KB | c88b04c28b8bbc96e4eea190e69d2671 |
| ENCFF082MXZ.tabix.bed.gz.tbi | 159.31 KB | 225aadc7ea205e7070216799c2e01515 |
| genomic_resource.yaml | 2.67 KB | 01bf6a8c07243e90f631344cfca69ec6 |
| statistics/ |