Resource
| Id | DNase-seq/ENCSR588JXI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR588JXI [biosample_summary="Homo sapiens left renal cortex interstitium tissue male embryo (105 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (105 days) output_type: peaks audit_warning: Alignment file {ENCFF027HRH|/files/ENCFF027HRH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 37780261 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 {ENCFF027HRH|/files/ENCFF027HRH/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.31. 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_ENCSR588JXI | float |
DNase-seq_ENCSR588JXI |
DNase-seq ENCSR588JXI [biosample_summary="Homo sapiens left renal cortex interstitium tissue male embryo (105 days)"]
|
 |
[0.213, 9.14] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7920239 | 0.25% | 38265 |
| chr1 | 708995 | 0.28% | 3318 |
| chr2 | 670463 | 0.28% | 3208 |
| chr3 | 529513 | 0.27% | 2592 |
| chr4 | 449683 | 0.24% | 2164 |
| chr5 | 479637 | 0.26% | 2343 |
| chr6 | 526173 | 0.31% | 2478 |
| chr7 | 390856 | 0.25% | 1904 |
| chr8 | 349199 | 0.24% | 1698 |
| chr9 | 314269 | 0.23% | 1577 |
| chr10 | 370079 | 0.28% | 1802 |
| chr11 | 407458 | 0.30% | 1985 |
| chr12 | 420442 | 0.32% | 2014 |
| chr13 | 212726 | 0.19% | 1030 |
| chr14 | 257440 | 0.24% | 1183 |
| chr15 | 262811 | 0.26% | 1278 |
| chr16 | 226975 | 0.25% | 1132 |
| chr17 | 279067 | 0.34% | 1405 |
| chr18 | 180105 | 0.22% | 885 |
| chr19 | 343032 | 0.59% | 1550 |
| chr20 | 173541 | 0.27% | 881 |
| chr21 | 72027 | 0.15% | 337 |
| chr22 | 101522 | 0.20% | 532 |
| chrX | 182684 | 0.12% | 920 |
| chrY | 11542 | 0.02% | 49 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 38265 | 1 | 1260 | 206.98 | 181 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF342FLC.bed.gz | 377.21 KB | 06014582660222c58db3375e92069689 |
| ENCFF342FLC.tabix.bed.gz | 350.15 KB | 809aa8b4e2779efe6bbe6bb81b8939b9 |
| ENCFF342FLC.tabix.bed.gz.tbi | 182.46 KB | 401d5a42f7aefba96eef8049cf9ab12e |
| genomic_resource.yaml | 2.72 KB | d812c503302a1340e292dfa20c3875d5 |
| statistics/ |