| Accession | HsInv0097 | Region of the inversion | chr3:109202512-109224821 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 21,760 bp | Supporting predictions | 4 |
| Inverted allele frequency | 0.0556 | Mechanism of origin | NHEJ or FoSTeS |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr3:109202512-109202535 |
| Ancestral orientation | NA | Breakpoint 2 | chr3:109223744-109224821 |
| Comments | Inverted allele includes two deletions of 24 bp and 1.1 kb flanking the inverted region
|
||
|
|
 |
|
|
Human Polymorphic Inversion DataBase
|
General information
- Region map
+ Predictions
| Description | Integrated analysis of structural variants in 2,504 human genomes through short-read and long-read DNA sequencing and statistical imputation using the 1000 Genomes Project data | ||||||||||
| Method | Paired-end mapping (PEM), Long-read sequencing | ||||||||||
| Name | |||
| Breakpoint 1 | chr3:109202531-109202531 | Breakpoint 2 | chr3:109223758-109223758 |
| Individuals | 18 out of 2504 individuals
 | ||
| Description | Paired-end mapping of 3-kb fragments in an African and in a putatively European individual with some predictions validated by PCR, fiber-FISH or comparison with Celera assembly | ||||||||||||||||||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||||||||||||||||||
| Name | |||||||||
| Breakpoint 1 | chr3:109201861-109201861 | Breakpoint 2 | chr3:109221546-109221546 | ||||||
| Individuals |
| ||||||||
| Name | |||||||||
| Breakpoint 1 | chr3:109204441-109204441 | Breakpoint 2 | chr3:109226060-109226060 | ||||||
| Individuals |
| ||||||||
- Martinez-Fundichely et al. 2014 (in preparation)
| Description | Accurate prediction of inversions in the human genome from Kidd et al. 2008 fosmid paired-end mapping data using the GRIAL algorithm, and validation of some predictions by sequence analysis and PCR | ||||||||||||||||||||||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||||||||||||||||||||||
| Name | |||||||||||||||||||||||
| Breakpoint 1 | chr3:109180872-109205531 | Breakpoint 2 | chr3:109222540-109254220 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.96657 | ||||||||||||||||||||
| Support | 6 probes | ||||||||||||||||||||||
| Individuals |
| ||||||||||||||||||||||
+ Validation and genotyping
| Description | Paired-end mapping of 3-kb fragments in an African and in a putatively European individual with some predictions validated by PCR, fiber-FISH or comparison with Celera assembly | ||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
-Martinez-Fundichely et al. 2014 (in preparation)
| Description | Accurate prediction of inversions in the human genome from Kidd et al. 2008 fosmid paired-end mapping data using the GRIAL algorithm, and validation of some predictions by sequence analysis and PCR | ||||
| Method | Polymerase chain reaction (PCR) |
| Status | Validated |
| Genotyping | 10 individuals: 8 HapMap/1000GP, 2 Other 8 STD/STD - 1 STD/INV - 1 ND |
- Frequency
|
|
+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
|
Yoruba in Ibadan, Nigeria (YRI) (Martinez-Fundichely et al. 2014 (in preparation)) | 4 | 0 | 1.0000 | 0.0000 | NA |
| Africa (AFR)
|
Africa (AFR) summary | 4 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
|
Utah residents with Northern and Western European ancestry (CEU) (Martinez-Fundichely et al. 2014 (in preparation)) | 2 | 0 | 1.0000 | 0.0000 | NA |
| Europe (EUR)
|
Europe (EUR) summary | 2 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
|
Han Chinese in Beijing, China (CHB) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 0 | 1.0000 | 0.0000 | NA |
| Japanese
|
Japanese in Tokyo, Japan (JPT) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 0 | 1.0000 | 0.0000 | NA |
| East Asia (EAS)
|
East Asia (EAS) summary | 2 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
|
Unknown (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
| Unknown
|
Unknown summary | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
|---|
+ Breakpoints
| Breakpoint 1 | chr3:109202512-109202535 | Breakpoint 2 | chr3:109223744-109224821 | ||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||||
| Description | Breakpoints defined by comparison with two sequenced fosmids | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NHEJ or FoSTeS
|
||||
| Flexibility | 9.95 | GC content | 0.46 | Stability | 1.88 |
| Comments |
Inverted region is flanked by two deletions of 24 bp and 1.1 kb, and was probably generated by NHEJ or FoSTeS events with no microhomology. Breakpoint positions comprise each deleted sequence. |
||
+ Evolutionary history
| Ancestral allele | NA | Age | ND |
| Derived allele | NA | Origin | ND |
+ Orientation in other species
Not defined
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
- 2017-09-18 00:00:00
| Breakpoint 1 | chr3:109197631-109205531 | Breakpoint 2 | chr3:109222540-109228356 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:32
| Breakpoint 1 | chr3:109197631-109205531 | Breakpoint 2 | chr3:109222540-109228356 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:32
| Breakpoint 1 | chr3:109202512-109202535 | Breakpoint 2 | chr3:109223744-109224821 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with two sequenced fosmids | ||
| Definition method | Manual curation | ||
Hosted by the Comparative and Functional Genomics group at the Universitat Autònoma de Barcelona
Contact us at invfestdb@uab.cat
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.