Resource
| Id | DNase-seq/ENCSR261SMF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR261SMF [biosample_summary="Homo sapiens iPS DF 6.9"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: peaks audit_warning: Alignment file {ENCFF123FCM|/files/ENCFF123FCM/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 22082019 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 {ENCFF123FCM|/files/ENCFF123FCM/} 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_ENCSR261SMF | float |
DNase-seq_ENCSR261SMF |
DNase-seq ENCSR261SMF [biosample_summary="Homo sapiens iPS DF 6.9"]
|
 |
[0.318, 11] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 6727288 | 0.21% | 40413 |
| chr1 | 626750 | 0.25% | 3736 |
| chr2 | 520960 | 0.22% | 3158 |
| chr3 | 440840 | 0.22% | 2694 |
| chr4 | 338157 | 0.18% | 2083 |
| chr5 | 360017 | 0.20% | 2207 |
| chr6 | 389376 | 0.23% | 2322 |
| chr7 | 349508 | 0.22% | 2091 |
| chr8 | 306320 | 0.21% | 1885 |
| chr9 | 277826 | 0.20% | 1680 |
| chr10 | 308169 | 0.23% | 1871 |
| chr11 | 349631 | 0.26% | 2114 |
| chr12 | 354018 | 0.27% | 2095 |
| chr13 | 171112 | 0.15% | 1028 |
| chr14 | 210789 | 0.20% | 1256 |
| chr15 | 206457 | 0.20% | 1243 |
| chr16 | 229390 | 0.25% | 1369 |
| chr17 | 277341 | 0.33% | 1599 |
| chr18 | 146901 | 0.18% | 922 |
| chr19 | 321461 | 0.55% | 1755 |
| chr20 | 178889 | 0.28% | 1076 |
| chr21 | 71936 | 0.15% | 437 |
| chr22 | 116078 | 0.23% | 693 |
| chrX | 166355 | 0.11% | 1039 |
| chrY | 9007 | 0.02% | 60 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 40413 | 8 | 804 | 166.46 | 160 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF668UYX.bed.gz | 417.94 KB | 4dced2e7d5f92207c41578234677487f |
| ENCFF668UYX.tabix.bed.gz | 367.42 KB | b8b77c56b95058d184d23cf5e91e71fb |
| ENCFF668UYX.tabix.bed.gz.tbi | 266.7 KB | 89a7e925ad10b90d6f708da80e9b69c6 |
| genomic_resource.yaml | 2.57 KB | 065d93372458415ac00eadc6b060fb32 |
| statistics/ |