Resource
| Id | DNase-seq/ENCSR133SPH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR133SPH [biosample_summary="Homo sapiens large intestine tissue female embryo (120 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (120 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN964FJP|/analyses/ENCAN964FJP/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF521WIQ|/files/ENCFF521WIQ/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 29710972 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/}) audit_warning: Alignment file {ENCFF541OSD|/files/ENCFF541OSD/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 29464215 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/}) 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 {ENCFF541OSD|/files/ENCFF541OSD/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.37. 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_ENCSR133SPH | float |
DNase-seq_ENCSR133SPH |
DNase-seq ENCSR133SPH [biosample_summary="Homo sapiens large intestine tissue female embryo (120 days)"]
|
 |
[4, 1.43e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 13146580 | 0.41% | 87487 |
| chr1 | 1244250 | 0.50% | 8279 |
| chr2 | 1067158 | 0.44% | 7106 |
| chr3 | 861779 | 0.43% | 5737 |
| chr4 | 695700 | 0.37% | 4626 |
| chr5 | 718200 | 0.40% | 4777 |
| chr6 | 815960 | 0.48% | 5432 |
| chr7 | 668964 | 0.42% | 4449 |
| chr8 | 575300 | 0.40% | 3827 |
| chr9 | 532650 | 0.38% | 3547 |
| chr10 | 619264 | 0.46% | 4119 |
| chr11 | 687442 | 0.51% | 4571 |
| chr12 | 658152 | 0.49% | 4383 |
| chr13 | 342128 | 0.30% | 2278 |
| chr14 | 419850 | 0.39% | 2796 |
| chr15 | 410340 | 0.40% | 2731 |
| chr16 | 428797 | 0.47% | 2855 |
| chr17 | 544907 | 0.65% | 3627 |
| chr18 | 310165 | 0.39% | 2064 |
| chr19 | 437757 | 0.75% | 2915 |
| chr20 | 326250 | 0.51% | 2169 |
| chr21 | 146850 | 0.31% | 978 |
| chr22 | 243845 | 0.48% | 1621 |
| chrX | 389522 | 0.25% | 2591 |
| chrY | 1350 | <0.01% | 9 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 87487 | 65 | 432 | 150.27 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF472DJP.bed.gz | 851.83 KB | 7605214c600c2846fa7ac0d2bf5f4660 |
| ENCFF472DJP.tabix.bed.gz | 730.77 KB | bd1e6922458252d5e32e269a31a0559b |
| ENCFF472DJP.tabix.bed.gz.tbi | 429.51 KB | 789a3f1d1c223ea548f753f46b4414bb |
| genomic_resource.yaml | 3.41 KB | 500a2699ecbd841265c1b155f37fa742 |
| statistics/ |