Resource
| Id | DNase-seq/ENCSR540PVZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR540PVZ [biosample_summary="Homo sapiens right renal pelvis tissue male embryo (120 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (120 days) output_type: peaks audit_warning: Replicate 1_3 has no significant footprints detected. audit_warning: Alignment file {ENCFF110OQK|/files/ENCFF110OQK/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 26201658 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 {ENCFF110OQK|/files/ENCFF110OQK/} 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR540PVZ | float |
DNase-seq_ENCSR540PVZ |
DNase-seq ENCSR540PVZ [biosample_summary="Homo sapiens right renal pelvis tissue male embryo (120 days)"]
|
 |
[0.268, 17.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8089945 | 0.25% | 45151 |
| chr1 | 760334 | 0.31% | 4223 |
| chr2 | 636491 | 0.26% | 3612 |
| chr3 | 531529 | 0.27% | 2970 |
| chr4 | 397820 | 0.21% | 2222 |
| chr5 | 436161 | 0.24% | 2451 |
| chr6 | 480991 | 0.28% | 2687 |
| chr7 | 403754 | 0.25% | 2276 |
| chr8 | 356999 | 0.25% | 2017 |
| chr9 | 332768 | 0.24% | 1882 |
| chr10 | 374062 | 0.28% | 2124 |
| chr11 | 424041 | 0.31% | 2355 |
| chr12 | 412296 | 0.31% | 2256 |
| chr13 | 202314 | 0.18% | 1150 |
| chr14 | 262913 | 0.25% | 1447 |
| chr15 | 264447 | 0.26% | 1475 |
| chr16 | 271440 | 0.30% | 1520 |
| chr17 | 338802 | 0.41% | 1874 |
| chr18 | 172602 | 0.21% | 991 |
| chr19 | 397727 | 0.68% | 2022 |
| chr20 | 207584 | 0.32% | 1192 |
| chr21 | 88986 | 0.19% | 507 |
| chr22 | 140435 | 0.28% | 777 |
| chrX | 188070 | 0.12% | 1085 |
| chrY | 7379 | 0.01% | 36 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 45151 | 2 | 740 | 179.18 | 176 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF046KDM.bed.gz | 474.53 KB | ea9a01bc15f59054405fd3923f00c6a9 |
| ENCFF046KDM.tabix.bed.gz | 423.25 KB | 180b66eec706304c8ef845c7f03e1363 |
| ENCFF046KDM.tabix.bed.gz.tbi | 263.37 KB | 5cbe327f6a0a753de6e0bcc57fa5b827 |
| genomic_resource.yaml | 2.76 KB | f09221a775897215d9f2402bc98e2170 |
| statistics/ |