Resource
| Id | DNase-seq/ENCSR956NOL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR956NOL [biosample_summary="Homo sapiens muscle of arm tissue male embryo (127 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (127 days) output_type: peaks audit_error: Alignment file {ENCFF044YTH|/files/ENCFF044YTH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 19209462 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: Replicate 1_1 has no significant footprints detected. 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 {ENCFF044YTH|/files/ENCFF044YTH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.35. 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_ENCSR956NOL | float |
DNase-seq_ENCSR956NOL |
DNase-seq ENCSR956NOL [biosample_summary="Homo sapiens muscle of arm tissue male embryo (127 days)"]
|
 |
[0.365, 14.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4380223 | 0.14% | 21987 |
| chr1 | 405670 | 0.16% | 1984 |
| chr2 | 345453 | 0.14% | 1738 |
| chr3 | 291061 | 0.15% | 1458 |
| chr4 | 225181 | 0.12% | 1134 |
| chr5 | 248006 | 0.14% | 1249 |
| chr6 | 281023 | 0.16% | 1380 |
| chr7 | 201494 | 0.13% | 1047 |
| chr8 | 185799 | 0.13% | 967 |
| chr9 | 181165 | 0.13% | 930 |
| chr10 | 200853 | 0.15% | 1051 |
| chr11 | 223178 | 0.17% | 1105 |
| chr12 | 232348 | 0.17% | 1145 |
| chr13 | 107032 | 0.09% | 549 |
| chr14 | 151980 | 0.14% | 755 |
| chr15 | 136043 | 0.13% | 689 |
| chr16 | 142415 | 0.16% | 729 |
| chr17 | 181642 | 0.22% | 903 |
| chr18 | 80900 | 0.10% | 439 |
| chr19 | 235389 | 0.40% | 1056 |
| chr20 | 105005 | 0.16% | 544 |
| chr21 | 48667 | 0.10% | 254 |
| chr22 | 78360 | 0.15% | 410 |
| chrX | 86201 | 0.06% | 444 |
| chrY | 5358 | 0.01% | 27 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 21987 | 3 | 900 | 199.22 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF637NQZ.bed.gz | 222.36 KB | d3d6b2dd26bd221ee956ac3b438b7a80 |
| ENCFF637NQZ.tabix.bed.gz | 200.45 KB | 97c28e817a621c491d59335ac5fc6859 |
| ENCFF637NQZ.tabix.bed.gz.tbi | 133.96 KB | 7820fdc21cc3210607bfb8ed4fc12266 |
| genomic_resource.yaml | 2.74 KB | afaadfdd8f125a4943acf6df3aa4748b |
| statistics/ |