Resource
| Id | DNase-seq/ENCSR158YXM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR158YXM [biosample_summary="Homo sapiens liver tissue embryo (59 days) and embryo (80 days)"] |
| Description |
status: released biological_replicates: Rep 2 summary: embryo (80 days) embryo (59 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 {ENCFF454GBD|/files/ENCFF454GBD/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.19. 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/}) 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 {ENCFF093KQP|/files/ENCFF093KQP/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.23. 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_ENCSR158YXM | float |
DNase-seq_ENCSR158YXM |
DNase-seq ENCSR158YXM [biosample_summary="Homo sapiens liver tissue embryo (59 days) and embryo (80 days)"]
|
 |
[0.0247, 18.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 17882876 | 0.56% | 93628 |
| chr1 | 1813272 | 0.73% | 9361 |
| chr2 | 1328156 | 0.55% | 7005 |
| chr3 | 1128370 | 0.57% | 5899 |
| chr4 | 755507 | 0.40% | 3947 |
| chr5 | 922450 | 0.51% | 4786 |
| chr6 | 1103072 | 0.65% | 5659 |
| chr7 | 874808 | 0.55% | 4628 |
| chr8 | 732470 | 0.50% | 3883 |
| chr9 | 734421 | 0.53% | 3859 |
| chr10 | 810354 | 0.61% | 4239 |
| chr11 | 929762 | 0.69% | 4904 |
| chr12 | 911808 | 0.68% | 4691 |
| chr13 | 405987 | 0.35% | 2157 |
| chr14 | 584143 | 0.55% | 3055 |
| chr15 | 593893 | 0.58% | 3134 |
| chr16 | 620069 | 0.69% | 3282 |
| chr17 | 896559 | 1.08% | 4676 |
| chr18 | 335709 | 0.42% | 1778 |
| chr19 | 842867 | 1.44% | 4354 |
| chr20 | 471771 | 0.73% | 2533 |
| chr21 | 200387 | 0.43% | 1047 |
| chr22 | 395403 | 0.78% | 2115 |
| chrX | 491024 | 0.31% | 2632 |
| chrY | 614 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 93628 | 3 | 860 | 191 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF760SUM.bed.gz | 1.02 MB | 47896a6df6746575ae7544ddff4e42c8 |
| ENCFF760SUM.tabix.bed.gz | 955.15 KB | 9bf1a8578a8f20079cb1ebc14c81c3de |
| ENCFF760SUM.tabix.bed.gz.tbi | 374.12 KB | 1b4ea75b094b5659bb451e4f9921ea63 |
| genomic_resource.yaml | 2.9 KB | fce268a0a46177c9a9c249d7a25bff1e |
| statistics/ |