Resource
| Id | DNase-seq/ENCSR000EMM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EMM [biosample_summary="Homo sapiens naive thymus-derived CD4-positive, alpha-beta T cell female adult (35 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (35 years) output_type: peaks audit_error: Alignment file {ENCFF252OHE|/files/ENCFF252OHE/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 19615721 mapped reads. According to ENCODE standards, conventional DNase-seq profile requires a minimum of 20 million uniquely mapped reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million uniquely mapped reads are recommended. (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 {ENCFF252OHE|/files/ENCFF252OHE/} 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_ENCSR000EMM | float |
DNase-seq_ENCSR000EMM |
DNase-seq ENCSR000EMM [biosample_summary="Homo sapiens naive thymus-derived CD4-positive, alpha-beta T cell female adult (35 years)"]
|
 |
[0.358, 17] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 3378801 | 0.11% | 18953 |
| chr1 | 342501 | 0.14% | 1887 |
| chr2 | 246275 | 0.10% | 1393 |
| chr3 | 210245 | 0.11% | 1185 |
| chr4 | 144174 | 0.08% | 796 |
| chr5 | 164469 | 0.09% | 935 |
| chr6 | 211682 | 0.12% | 1163 |
| chr7 | 172641 | 0.11% | 978 |
| chr8 | 121904 | 0.08% | 709 |
| chr9 | 126682 | 0.09% | 724 |
| chr10 | 153228 | 0.11% | 856 |
| chr11 | 170641 | 0.13% | 955 |
| chr12 | 184386 | 0.14% | 1028 |
| chr13 | 74472 | 0.07% | 402 |
| chr14 | 118391 | 0.11% | 660 |
| chr15 | 107515 | 0.11% | 624 |
| chr16 | 114272 | 0.13% | 647 |
| chr17 | 166866 | 0.20% | 945 |
| chr18 | 54686 | 0.07% | 308 |
| chr19 | 210534 | 0.36% | 1130 |
| chr20 | 85304 | 0.13% | 486 |
| chr21 | 40179 | 0.09% | 225 |
| chr22 | 63152 | 0.12% | 365 |
| chrX | 94322 | 0.06% | 550 |
| chrY | 280 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 18953 | 5 | 820 | 178.27 | 160 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF191VQI.bed.gz | 197.43 KB | 9644eb24959b70108a24946f8002310e |
| ENCFF191VQI.tabix.bed.gz | 176.28 KB | 7a3faa0226359d8ecb587b46987ba4b8 |
| ENCFF191VQI.tabix.bed.gz.tbi | 134.58 KB | 2fe80e8db204ea22d9901cdbb8003e88 |
| genomic_resource.yaml | 2.76 KB | 365a5e4297a9fb9e8da3e8df74e11eba |
| statistics/ |