Resource
| Id | DNase-seq/ENCSR214QEO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR214QEO [biosample_summary="Homo sapiens large intestine tissue female embryo (91 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (91 days) output_type: peaks audit_warning: Alignment file {ENCFF268WPW|/files/ENCFF268WPW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 34249961 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 {ENCFF268WPW|/files/ENCFF268WPW/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.34. 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_ENCSR214QEO | float |
DNase-seq_ENCSR214QEO |
DNase-seq ENCSR214QEO [biosample_summary="Homo sapiens large intestine tissue female embryo (91 days)"]
|
 |
[0.235, 15.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9067180 | 0.28% | 46670 |
| chr1 | 843115 | 0.34% | 4345 |
| chr2 | 708590 | 0.29% | 3698 |
| chr3 | 598791 | 0.30% | 3108 |
| chr4 | 473845 | 0.25% | 2453 |
| chr5 | 474055 | 0.26% | 2427 |
| chr6 | 551820 | 0.32% | 2828 |
| chr7 | 472808 | 0.30% | 2458 |
| chr8 | 402456 | 0.28% | 2107 |
| chr9 | 370414 | 0.27% | 1910 |
| chr10 | 412797 | 0.31% | 2157 |
| chr11 | 464149 | 0.34% | 2417 |
| chr12 | 468598 | 0.35% | 2373 |
| chr13 | 229373 | 0.20% | 1188 |
| chr14 | 301340 | 0.28% | 1523 |
| chr15 | 280814 | 0.28% | 1467 |
| chr16 | 296334 | 0.33% | 1545 |
| chr17 | 393743 | 0.47% | 1982 |
| chr18 | 213159 | 0.27% | 1105 |
| chr19 | 400809 | 0.68% | 1900 |
| chr20 | 220671 | 0.34% | 1129 |
| chr21 | 99801 | 0.21% | 514 |
| chr22 | 157263 | 0.31% | 814 |
| chrX | 231902 | 0.15% | 1218 |
| chrY | 533 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 46670 | 3 | 760 | 194.28 | 194 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF180VCG.bed.gz | 490.0 KB | a098e38c4de75e3d7cfeb7f86ef6664a |
| ENCFF180VCG.tabix.bed.gz | 438.24 KB | 2dd9414e8e08d9d5fb5a79044cad237e |
| ENCFF180VCG.tabix.bed.gz.tbi | 259.01 KB | 10176fc51d2129c4e819b11fce77ce8f |
| genomic_resource.yaml | 2.67 KB | cc239bf93286fb3b93e3b1367214d79b |
| statistics/ |