Resource
| Id | DNase-seq/ENCSR435NHO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR435NHO [biosample_summary="Homo sapiens embryonic facial prominence tissue embryo (53 days) and embryo (58 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: embryo (53 days) embryo (58 days) output_type: peaks audit_error: 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 {ENCFF967NGX|/files/ENCFF967NGX/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) for GRCh38 assembly have a SPOT1 score of 0.18. 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/}) audit_error: 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 {ENCFF603DLI|/files/ENCFF603DLI/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) for GRCh38 assembly have a SPOT1 score of 0.25. 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/}) audit_internal_action: Archived analysis {ENCAN301NSI|/analyses/ENCAN301NSI/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR435NHO | float |
DNase-seq_ENCSR435NHO |
DNase-seq ENCSR435NHO [biosample_summary="Homo sapiens embryonic facial prominence tissue embryo (53 days) and embryo (58 days)"]
|
 |
[7, 3.5e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 15085447 | 0.47% | 100334 |
| chr1 | 1363123 | 0.55% | 9062 |
| chr2 | 1217468 | 0.50% | 8101 |
| chr3 | 970584 | 0.49% | 6452 |
| chr4 | 789113 | 0.41% | 5239 |
| chr5 | 858279 | 0.47% | 5705 |
| chr6 | 942373 | 0.55% | 6269 |
| chr7 | 766158 | 0.48% | 5096 |
| chr8 | 705091 | 0.49% | 4690 |
| chr9 | 666452 | 0.48% | 4431 |
| chr10 | 756560 | 0.57% | 5030 |
| chr11 | 759466 | 0.56% | 5051 |
| chr12 | 737879 | 0.55% | 4911 |
| chr13 | 418246 | 0.37% | 2779 |
| chr14 | 488058 | 0.46% | 3247 |
| chr15 | 467907 | 0.46% | 3117 |
| chr16 | 480268 | 0.53% | 3195 |
| chr17 | 613578 | 0.74% | 4087 |
| chr18 | 341582 | 0.42% | 2267 |
| chr19 | 511118 | 0.87% | 3403 |
| chr20 | 392426 | 0.61% | 2613 |
| chr21 | 186008 | 0.40% | 1238 |
| chr22 | 254073 | 0.50% | 1693 |
| chrX | 398437 | 0.26% | 2650 |
| chrY | 1200 | <0.01% | 8 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 100334 | 13 | 450 | 150.35 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF440BEP.bed.gz | 982.59 KB | 23ad093aabb0934a0d1b267ad6ca7e75 |
| ENCFF440BEP.tabix.bed.gz | 839.54 KB | e865c6ed65f90642ee823481618eedb7 |
| ENCFF440BEP.tabix.bed.gz.tbi | 439.25 KB | 0bf4124f3bb309cb9130b90963065ab3 |
| genomic_resource.yaml | 3.11 KB | c8f5e87c275589e24d2481705ebba712 |
| statistics/ |