| Accession | HsInv0114 | Region of the inversion | chr9:125778473-125795872 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 14,667 bp | Supporting predictions | 3 |
| Inverted allele frequency | 0.6161 | Mechanism of origin | NAHR |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr9:125778473-125781206 |
| Ancestral orientation | Inverted | Breakpoint 2 | chr9:125793139-125795872 |
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
| Description | Paired-end mapping analysis of the J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr9:125778562-125780830 | Breakpoint 2 | chr9:125791433-125797154 | ||||
| Individuals |
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| 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 | chr9:125778256-125778256 | Breakpoint 2 | chr9:125792519-125792519 | ||||||
| Individuals |
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- 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 | chr9:125754527-125780860 | Breakpoint 2 | chr9:125794813-125821471 | ||||||||||||||||||||
| D/C Score | 0.54 | Disc. Support Prob. | 0.99998 | ||||||||||||||||||||
| Support | 40 probes  | ||||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| Description | Validation and genotyping of 22 inversion predictions by inverse PCR | ||||
| Method | Inverse polymerase chain reaction (iPCR) |
| Status | Validated |
| Genotyping | 77 individuals: 76 HapMap/1000GP, 1 Other 13 STD/STD - 34 STD/INV - 30 INV/INV |
| 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 | Fosmid sequence analysis |
| Status | Validated |
- Frequency
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+ Africa (AFR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
Yoruba
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Yoruba in Ibadan, Nigeria (YRI) (Aguado et al. 2014) | 4 | 2 | 0.7500 | 0.2500 | > 0.5 |
| Africa (AFR)
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Africa (AFR) summary | 4 | 2 | 0.7500 | 0.2500 | > 0.5 |
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+ Europe (EUR)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Northwestern European
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Utah residents with Northern and Western European ancestry (CEU) (Aguado et al. 2014) | 49 | 64 | 0.3469 | 0.6531 | > 0.5 |
| Europe (EUR)
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Europe (EUR) summary | 49 | 64 | 0.3469 | 0.6531 | > 0.5 |
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+ 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) (Aguado et al. 2014) | 1 | 0 | 1.0000 | 0.0000 | NA |
| Japanese
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Japanese in Tokyo, Japan (JPT) (Aguado et al. 2014) | 1 | 1 | 0.5000 | 0.5000 | > 0.3 |
| East Asia (EAS)
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East Asia (EAS) summary | 2 | 1 | 0.7500 | 0.2500 | > 0.5 |
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+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
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Unknown (Aguado et al. 2014) | 1 | 2 | 0.0000 | 1.0000 | NA |
| Unknown
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Unknown summary | 1 | 2 | 0.0000 | 1.0000 | NA |
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+ Breakpoints
| Breakpoint 1 | chr9:125778473-125781206 | Breakpoint 2 | chr9:125793139-125795872 | ||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||||
| Description | Breakpoints defined by comparison with two sequenced fosmids | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NAHR
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| Flexibility | 10.07 | GC content | 0.48 | Stability | 1.92 |
| Comments |
Inversion generated by non-allelic homologous recombination (NAHR) between 2.7 kb inverted SDs with almost 100% identity |
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+ Evolutionary history
| Ancestral allele | Inverted | Age | ND |
| Derived allele | Standard | Origin | ND |
+ Orientation in other species
| Species | Orientation | Method | Study |
| Chimpanzee | Inverted | Inverse polymerase chain reaction (iPCR) | Aguado et al. 2014 |
| Gorilla | Inverted | Inverse polymerase chain reaction (iPCR) | Aguado et al. 2014 |
+ Age
Not defined
+ Origin
Not defined
+ Functional effects
No genes disrupted by the inversion breakpoints
+ Inversion phenotypical effects
Not defined
+ Report history
- 2015-02-23 10:14:36
| Breakpoint 1 | chr9:125778562-125780830 | Breakpoint 2 | chr9:125794813-125797154 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:36
| Breakpoint 1 | chr9:125778473-125781206 | Breakpoint 2 | chr9:125793139-125795872 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by comparison with two sequenced fosmids | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:14:36
| Breakpoint 1 | chr9:125778562-125780830 | Breakpoint 2 | chr9:125794813-125797154 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:36
| Breakpoint 1 | chr9:125771446-125780860 | Breakpoint 2 | chr9:125794813-125799329 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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