Resource
| Id | DNase-seq/ENCSR888GBS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR888GBS [biosample_summary="Homo sapiens muscle of arm tissue male embryo (96 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (96 days) output_type: peaks audit_warning: Alignment file {ENCFF465GMC|/files/ENCFF465GMC/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 38103510 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 {ENCFF465GMC|/files/ENCFF465GMC/} 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_ENCSR888GBS | float |
DNase-seq_ENCSR888GBS |
DNase-seq ENCSR888GBS [biosample_summary="Homo sapiens muscle of arm tissue male embryo (96 days)"]
|
 |
[0.211, 10.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8847060 | 0.27% | 43028 |
| chr1 | 806809 | 0.32% | 3899 |
| chr2 | 689793 | 0.28% | 3401 |
| chr3 | 590842 | 0.30% | 2884 |
| chr4 | 465782 | 0.24% | 2223 |
| chr5 | 490825 | 0.27% | 2354 |
| chr6 | 580604 | 0.34% | 2821 |
| chr7 | 428699 | 0.27% | 2145 |
| chr8 | 402188 | 0.28% | 2018 |
| chr9 | 365901 | 0.26% | 1797 |
| chr10 | 400998 | 0.30% | 1943 |
| chr11 | 459392 | 0.34% | 2246 |
| chr12 | 461310 | 0.35% | 2200 |
| chr13 | 246677 | 0.22% | 1225 |
| chr14 | 307500 | 0.29% | 1449 |
| chr15 | 280468 | 0.27% | 1397 |
| chr16 | 271654 | 0.30% | 1336 |
| chr17 | 360923 | 0.43% | 1741 |
| chr18 | 192552 | 0.24% | 962 |
| chr19 | 384601 | 0.66% | 1722 |
| chr20 | 210556 | 0.33% | 1052 |
| chr21 | 100430 | 0.22% | 494 |
| chr22 | 137426 | 0.27% | 668 |
| chrX | 203334 | 0.13% | 1014 |
| chrY | 7796 | 0.01% | 37 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 43028 | 3 | 1080 | 205.61 | 189 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF010APV.bed.gz | 440.58 KB | 7406edf5b197e64eada83ecdb8d4e4d4 |
| ENCFF010APV.tabix.bed.gz | 399.82 KB | 721d243639dd373c9c0d6780f325c08b |
| ENCFF010APV.tabix.bed.gz.tbi | 237.27 KB | 0e1d8ee6f95cf7ae60c4748b2e72086d |
| genomic_resource.yaml | 2.66 KB | ea2d7a3e0bdeb4585cd1f44fbfd11cc2 |
| statistics/ |