Resource
| Id | DNase-seq/ENCSR826URD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR826URD [biosample_summary="Homo sapiens neural crest cell"] |
| Description |
status: released biological_replicates: Rep 2 summary: female embryo (5 days) output_type: peaks audit_warning: Alignment file {ENCFF103QUR|/files/ENCFF103QUR/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 23902110 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 {ENCFF916YHM|/files/ENCFF916YHM/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.30. 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_ENCSR826URD | float |
DNase-seq_ENCSR826URD |
DNase-seq ENCSR826URD [biosample_summary="Homo sapiens neural crest cell"]
|
 |
[0.0897, 15.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12989373 | 0.40% | 61741 |
| chr1 | 1268710 | 0.51% | 5919 |
| chr2 | 945086 | 0.39% | 4480 |
| chr3 | 748949 | 0.38% | 3577 |
| chr4 | 542491 | 0.29% | 2579 |
| chr5 | 638789 | 0.35% | 3071 |
| chr6 | 733852 | 0.43% | 3452 |
| chr7 | 633016 | 0.40% | 3023 |
| chr8 | 532686 | 0.37% | 2549 |
| chr9 | 547944 | 0.40% | 2621 |
| chr10 | 593308 | 0.44% | 2839 |
| chr11 | 705406 | 0.52% | 3328 |
| chr12 | 653247 | 0.49% | 3095 |
| chr13 | 281303 | 0.25% | 1346 |
| chr14 | 414859 | 0.39% | 1930 |
| chr15 | 449079 | 0.44% | 2165 |
| chr16 | 486533 | 0.54% | 2351 |
| chr17 | 676657 | 0.81% | 3187 |
| chr18 | 268005 | 0.33% | 1278 |
| chr19 | 694039 | 1.18% | 3231 |
| chr20 | 363754 | 0.56% | 1785 |
| chr21 | 129340 | 0.28% | 617 |
| chr22 | 277443 | 0.55% | 1359 |
| chrX | 404780 | 0.26% | 1958 |
| chrY | 97 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 61741 | 1 | 1020 | 210.38 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF305UGC.bed.gz | 667.84 KB | ea3a3712ea9a23537aca8d8057010b6f |
| ENCFF305UGC.tabix.bed.gz | 618.91 KB | 9c377dd2d3a5dd508de8a03502d4e570 |
| ENCFF305UGC.tabix.bed.gz.tbi | 291.02 KB | ce40103b040247ae743294670a6db7e6 |
| genomic_resource.yaml | 2.58 KB | 33a74ee0065b10204984d53b998e6d09 |
| statistics/ |