Resource
| Id | DNase-seq/ENCSR562FNN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR562FNN [biosample_summary="Homo sapiens liver tissue female embryo (101 days) and female embryo (113 days)"] |
| Description |
status: archived biological_replicates: Rep 1 summary: female embryo (101 days) female embryo (113 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN581WCZ|/analyses/ENCAN581WCZ/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} 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 {ENCFF191SRN|/files/ENCFF191SRN/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) for GRCh38 assembly have a SPOT1 score of 0.33. 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_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 {ENCFF815OAG|/files/ENCFF815OAG/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR562FNN | float |
DNase-seq_ENCSR562FNN |
DNase-seq ENCSR562FNN [biosample_summary="Homo sapiens liver tissue female embryo (101 days) and female embryo (113 days)"]
|
 |
[1, 5.86e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 38022192 | 1.18% | 252339 |
| chr1 | 3480569 | 1.40% | 23116 |
| chr2 | 3448226 | 1.42% | 22882 |
| chr3 | 2126056 | 1.07% | 14110 |
| chr4 | 1197190 | 0.63% | 7935 |
| chr5 | 1896373 | 1.04% | 12588 |
| chr6 | 1869250 | 1.09% | 12417 |
| chr7 | 1830559 | 1.15% | 12148 |
| chr8 | 1671684 | 1.15% | 11093 |
| chr9 | 1693076 | 1.22% | 11246 |
| chr10 | 2413713 | 1.80% | 16019 |
| chr11 | 1962830 | 1.45% | 13010 |
| chr12 | 1441274 | 1.08% | 9557 |
| chr13 | 841194 | 0.74% | 5577 |
| chr14 | 1192053 | 1.11% | 7919 |
| chr15 | 1434851 | 1.41% | 9523 |
| chr16 | 1407669 | 1.56% | 9349 |
| chr17 | 1602062 | 1.92% | 10624 |
| chr18 | 924039 | 1.15% | 6140 |
| chr19 | 1464034 | 2.50% | 9721 |
| chr20 | 1288092 | 2.00% | 8552 |
| chr21 | 614562 | 1.32% | 4075 |
| chr22 | 979967 | 1.93% | 6506 |
| chrX | 1215119 | 0.78% | 8047 |
| chrY | 27750 | 0.05% | 185 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 252339 | 1 | 750 | 150.68 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF173YTQ.bed.gz | 2.29 MB | 43f79a810ad1c510302a58484fe134c6 |
| ENCFF173YTQ.tabix.bed.gz | 1.97 MB | 0324329e36888a97717606b967653575 |
| ENCFF173YTQ.tabix.bed.gz.tbi | 435.82 KB | 16826bc5653c33e032d007a05a3957c4 |
| genomic_resource.yaml | 3.13 KB | 091d185cbdd1265d7e6ca5f5dd5d2134 |
| statistics/ |