Resource
| Id | DNase-seq/ENCSR364TKL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR364TKL [biosample_summary="Homo sapiens renal pelvis tissue male embryo (97 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (97 days) output_type: peaks audit_warning: Alignment file {ENCFF520WIK|/files/ENCFF520WIK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 27764601 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_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 {ENCFF520WIK|/files/ENCFF520WIK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.40. 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_ENCSR364TKL | float |
DNase-seq_ENCSR364TKL |
DNase-seq ENCSR364TKL [biosample_summary="Homo sapiens renal pelvis tissue male embryo (97 days)"]
|
 |
[0.289, 18] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8665058 | 0.27% | 47779 |
| chr1 | 810615 | 0.33% | 4418 |
| chr2 | 676427 | 0.28% | 3765 |
| chr3 | 578103 | 0.29% | 3148 |
| chr4 | 451533 | 0.24% | 2478 |
| chr5 | 487384 | 0.27% | 2705 |
| chr6 | 515772 | 0.30% | 2842 |
| chr7 | 441746 | 0.28% | 2443 |
| chr8 | 401256 | 0.28% | 2205 |
| chr9 | 362878 | 0.26% | 2038 |
| chr10 | 411432 | 0.31% | 2280 |
| chr11 | 437548 | 0.32% | 2432 |
| chr12 | 437821 | 0.33% | 2393 |
| chr13 | 228315 | 0.20% | 1290 |
| chr14 | 279008 | 0.26% | 1502 |
| chr15 | 282079 | 0.28% | 1558 |
| chr16 | 276732 | 0.31% | 1533 |
| chr17 | 337465 | 0.41% | 1868 |
| chr18 | 190479 | 0.24% | 1071 |
| chr19 | 385967 | 0.66% | 1986 |
| chr20 | 226892 | 0.35% | 1299 |
| chr21 | 91578 | 0.20% | 523 |
| chr22 | 141857 | 0.28% | 797 |
| chrX | 205500 | 0.13% | 1172 |
| chrY | 6671 | 0.01% | 33 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 47779 | 1 | 960 | 181.36 | 176 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF039LHP.bed.gz | 500.3 KB | 4d98ee50981716f4863c0d45960256f4 |
| ENCFF039LHP.tabix.bed.gz | 445.87 KB | 3f8fe813ddff39891f9374fa040155ed |
| ENCFF039LHP.tabix.bed.gz.tbi | 273.81 KB | cb850572bf83d006a27e29cc48e77fbd |
| genomic_resource.yaml | 2.65 KB | b164c3e3342e2f0070dd9d9d1009e2b0 |
| statistics/ |