Resource
| Id | DNase-seq/ENCSR943SYS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR943SYS [biosample_summary="Homo sapiens H9 G2 phase stably expressing CDT1, stably expressing GMNN"] |
| Description |
status: released biological_replicates: Rep 1 summary: stably expressing C-terminal DsRed-tagged CDT1, stably expressing N-terminal eGFP-tagged GMNN G2 phase output_type: peaks audit_internal_action: Archived analysis {ENCAN633OPX|/analyses/ENCAN633OPX/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} 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 {ENCFF602SRQ|/files/ENCFF602SRQ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) for GRCh38 assembly have a SPOT1 score of 0.27. 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/}) 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 {ENCFF649ZAQ|/files/ENCFF649ZAQ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL202DNS|/pipelines/ENCPL202DNS/}) 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR943SYS | float |
DNase-seq_ENCSR943SYS |
DNase-seq ENCSR943SYS [biosample_summary="Homo sapiens H9 G2 phase stably expressing CDT1, stably expressing GMNN"]
|
 |
[1, 6.65e+04] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 38764164 | 1.20% | 257926 |
| chr1 | 3355790 | 1.35% | 22335 |
| chr2 | 3113819 | 1.29% | 20710 |
| chr3 | 2487724 | 1.25% | 16545 |
| chr4 | 2143474 | 1.13% | 14241 |
| chr5 | 2230788 | 1.23% | 14846 |
| chr6 | 2292959 | 1.34% | 15254 |
| chr7 | 2042762 | 1.28% | 13597 |
| chr8 | 1824482 | 1.26% | 12140 |
| chr9 | 1582728 | 1.14% | 10528 |
| chr10 | 1819308 | 1.36% | 12107 |
| chr11 | 1917147 | 1.42% | 12758 |
| chr12 | 1858923 | 1.39% | 12374 |
| chr13 | 1170637 | 1.02% | 7788 |
| chr14 | 1219089 | 1.14% | 8109 |
| chr15 | 1184965 | 1.16% | 7884 |
| chr16 | 1258558 | 1.39% | 8377 |
| chr17 | 1504258 | 1.81% | 10018 |
| chr18 | 874927 | 1.09% | 5821 |
| chr19 | 1260333 | 2.15% | 8385 |
| chr20 | 1011338 | 1.57% | 6733 |
| chr21 | 427191 | 0.91% | 2844 |
| chr22 | 643993 | 1.27% | 4288 |
| chrX | 1520071 | 0.97% | 10118 |
| chrY | 18900 | 0.03% | 126 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 257926 | 2 | 450 | 150.29 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF177DSB.bed.gz | 2.47 MB | b6c9fd261f95e05290a2ceadb69e4be6 |
| ENCFF177DSB.tabix.bed.gz | 2.12 MB | 96bc4ee5a1dc5fb7e804cbf537904ff3 |
| ENCFF177DSB.tabix.bed.gz.tbi | 756.49 KB | 8d5bdc391a8bc8d8dc5b966b91db5a39 |
| genomic_resource.yaml | 3.21 KB | 37c602d13278ffaadef532c433e36ae8 |
| statistics/ |