Resource
| Id | DNase-seq/ENCSR619BNL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR619BNL [biosample_summary="Homo sapiens muscle of arm tissue male embryo (97 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (97 days) output_type: peaks audit_warning: Alignment file {ENCFF161ZAX|/files/ENCFF161ZAX/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 33167191 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 {ENCFF161ZAX|/files/ENCFF161ZAX/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.31. 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_ENCSR619BNL | float |
DNase-seq_ENCSR619BNL |
DNase-seq ENCSR619BNL [biosample_summary="Homo sapiens muscle of arm tissue male embryo (97 days)"]
|
 |
[0.151, 8.08] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7652732 | 0.24% | 39696 |
| chr1 | 691337 | 0.28% | 3500 |
| chr2 | 609719 | 0.25% | 3213 |
| chr3 | 510683 | 0.26% | 2655 |
| chr4 | 390308 | 0.21% | 2024 |
| chr5 | 423604 | 0.23% | 2210 |
| chr6 | 487946 | 0.29% | 2463 |
| chr7 | 372448 | 0.23% | 1997 |
| chr8 | 352087 | 0.24% | 1829 |
| chr9 | 316059 | 0.23% | 1652 |
| chr10 | 355298 | 0.27% | 1887 |
| chr11 | 395958 | 0.29% | 2060 |
| chr12 | 401061 | 0.30% | 2080 |
| chr13 | 207413 | 0.18% | 1084 |
| chr14 | 262936 | 0.25% | 1307 |
| chr15 | 246721 | 0.24% | 1274 |
| chr16 | 232255 | 0.26% | 1235 |
| chr17 | 320531 | 0.38% | 1656 |
| chr18 | 164091 | 0.20% | 875 |
| chr19 | 338123 | 0.58% | 1616 |
| chr20 | 183819 | 0.29% | 987 |
| chr21 | 84947 | 0.18% | 448 |
| chr22 | 127357 | 0.25% | 677 |
| chrX | 170828 | 0.11% | 934 |
| chrY | 7203 | 0.01% | 33 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 39696 | 1 | 960 | 192.78 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF387YOJ.bed.gz | 405.75 KB | a35e2c9c8cfe0834fc7ae519aec01796 |
| ENCFF387YOJ.tabix.bed.gz | 367.19 KB | 1bebce90fe4fc527808eb1e94eaede45 |
| ENCFF387YOJ.tabix.bed.gz.tbi | 226.4 KB | 56ba563663ee646ff9e51b450e41dd3d |
| genomic_resource.yaml | 2.66 KB | 5957ad11f7bfd3890090e0b247f86dbe |
| statistics/ |