Resource
| Id | DNase-seq/ENCSR820ICX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR820ICX [biosample_summary="Homo sapiens retina tissue female embryo (89 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (89 days) output_type: peaks 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 {ENCFF842NAE|/files/ENCFF842NAE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) 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-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR820ICX | float |
DNase-seq_ENCSR820ICX |
DNase-seq ENCSR820ICX [biosample_summary="Homo sapiens retina tissue female embryo (89 days)"]
|
 |
[0.0211, 14] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 34716034 | 1.08% | 151331 |
| chr1 | 3099276 | 1.24% | 13353 |
| chr2 | 2812058 | 1.16% | 12177 |
| chr3 | 2165037 | 1.09% | 9450 |
| chr4 | 1812698 | 0.95% | 7894 |
| chr5 | 2000481 | 1.10% | 8721 |
| chr6 | 2055461 | 1.20% | 8791 |
| chr7 | 1826518 | 1.15% | 7945 |
| chr8 | 1603392 | 1.10% | 7043 |
| chr9 | 1441420 | 1.04% | 6301 |
| chr10 | 1701270 | 1.27% | 7415 |
| chr11 | 1794736 | 1.33% | 7783 |
| chr12 | 1657530 | 1.24% | 7180 |
| chr13 | 1052215 | 0.92% | 4494 |
| chr14 | 1146997 | 1.07% | 4999 |
| chr15 | 1109636 | 1.09% | 4850 |
| chr16 | 1138887 | 1.26% | 5029 |
| chr17 | 1434253 | 1.72% | 6334 |
| chr18 | 870610 | 1.08% | 3694 |
| chr19 | 1146935 | 1.96% | 5138 |
| chr20 | 917824 | 1.42% | 4046 |
| chr21 | 370957 | 0.79% | 1668 |
| chr22 | 584049 | 1.15% | 2638 |
| chrX | 972886 | 0.62% | 4379 |
| chrY | 908 | <0.01% | 9 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 151331 | 1 | 1360 | 229.4 | 207 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF910DCV.bed.gz | 1.59 MB | fb99464aeeff337dc859d678d8c8da7b |
| ENCFF910DCV.tabix.bed.gz | 1.48 MB | fe2408882d1cd73807308bbe51f6e898 |
| ENCFF910DCV.tabix.bed.gz.tbi | 549.41 KB | d7100fb048f2e1511e751adbfb5e4e47 |
| genomic_resource.yaml | 2.03 KB | c5d2f9d4d4207b55634b41cdecaa7012 |
| statistics/ |