Resource
| Id | DNase-seq/ENCSR037PGI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR037PGI [biosample_summary="Homo sapiens RCC 7860"] |
| Description |
status: released biological_replicates: Rep 1 summary: 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 {ENCFF499DRT|/files/ENCFF499DRT/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.38. 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_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 {ENCFF386XBC|/files/ENCFF386XBC/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.32. 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_ENCSR037PGI | float |
DNase-seq_ENCSR037PGI |
DNase-seq ENCSR037PGI [biosample_summary="Homo sapiens RCC 7860"]
|
 |
[0.0288, 153] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 26269577 | 0.82% | 132721 |
| chr1 | 2603133 | 1.05% | 13117 |
| chr2 | 2155995 | 0.89% | 10898 |
| chr3 | 1734316 | 0.87% | 8768 |
| chr4 | 1237213 | 0.65% | 6383 |
| chr5 | 1523221 | 0.84% | 7664 |
| chr6 | 1535020 | 0.90% | 7740 |
| chr7 | 1499580 | 0.94% | 7591 |
| chr8 | 1200817 | 0.83% | 6020 |
| chr9 | 1206582 | 0.87% | 6076 |
| chr10 | 1367514 | 1.02% | 6880 |
| chr11 | 1225562 | 0.91% | 6183 |
| chr12 | 1243949 | 0.93% | 6302 |
| chr13 | 603608 | 0.53% | 3096 |
| chr14 | 681171 | 0.64% | 3458 |
| chr15 | 858764 | 0.84% | 4363 |
| chr16 | 847991 | 0.94% | 4262 |
| chr17 | 1107749 | 1.33% | 5524 |
| chr18 | 546645 | 0.68% | 2803 |
| chr19 | 828476 | 1.41% | 4068 |
| chr20 | 684584 | 1.06% | 3459 |
| chr21 | 314857 | 0.67% | 1570 |
| chr22 | 494044 | 0.97% | 2496 |
| chrX | 708373 | 0.45% | 3676 |
| chrY | 60413 | 0.11% | 324 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 132721 | 1 | 780 | 197.93 | 200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF589UEE.bed.gz | 1.45 MB | 2d40818a104dcdc4ce107887a4f77b6d |
| ENCFF589UEE.tabix.bed.gz | 1.33 MB | b5d8d9574e0cc5a828b16d3ae64611d4 |
| ENCFF589UEE.tabix.bed.gz.tbi | 480.92 KB | 14c2e0f2b5087a1a2f31af1fc70c362b |
| genomic_resource.yaml | 2.77 KB | 0ef40dcda0204d7beb9b98c4b2fb1d58 |
| statistics/ |