| Accession | HsInv0272 | Region of the inversion | chr5:178799281-178862360 |
| Status | False | Prediction type | Simple |
| Estimated Inversion Size | 58,462 bp | Supporting predictions | 1 |
| Inverted allele frequency | NA | Mechanism of origin | NA |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr5:178799281-178807738 |
| Ancestral orientation | NA | Breakpoint 2 | chr5:178861581-178862360 |
| Comments | False inversion prediction possibly caused by incorrect paired-end mapping due to a region of sequence variation within SDs
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Human Polymorphic Inversion DataBase
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General information
- Region map
+ Predictions
- 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 | chr5:178799281-178807738 | Breakpoint 2 | chr5:178861581-178862360 | ||||||||||||||||||||
| D/C Score | -7.04 | Disc. Support Prob. | 0 | ||||||||||||||||||||
| Support | 6 probes  | ||||||||||||||||||||||
| Individuals |
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| Comments | Below the threshold of the Discordant/Concordant (D/C) ratio score. Below the threshold of the Discordant Support (DS) probability. Discordant PEM pattern caused by incorrect mapping of one end of all fosmids due to sequence variation within SDs. | ||||||||||||||||||||||
+ Validation and genotyping
| Description | Validation and genotyping of 22 inversion predictions by inverse PCR | ||||||
| Method | Inverse polymerase chain reaction (iPCR) |
| Status | False |
| Genotyping | 9 individuals: 8 HapMap/1000GP, 1 Other 9 STD/STD |
| Comment | Inverse PCR assays of both breakpoints indicates that there is not an inversion between the two SDs |
-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 | Sequence analysis |
| Status | False |
| Comment | Sequence analysis indicates that inversion prediction is caused by incorrect paired-end mapping due to a variable sequence region when comparing HG18 and HuRef SDs |
- 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 | 0 | 1.0000 | 0.0000 | NA |
| Africa (AFR)
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Africa (AFR) summary | 4 | 0 | 1.0000 | 0.0000 | NA |
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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) | 2 | 0 | 1.0000 | 0.0000 | NA |
| Europe (EUR)
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Europe (EUR) summary | 2 | 0 | 1.0000 | 0.0000 | NA |
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+ East Asia (EAS)
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Han Chinese
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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 | 0 | 1.0000 | 0.0000 | NA |
| East Asia (EAS)
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East Asia (EAS) summary | 2 | 0 | 1.0000 | 0.0000 | NA |
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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 | 0 | 1.0000 | 0.0000 | NA |
| Unknown
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Unknown summary | 1 | 0 | 1.0000 | 0.0000 | NA |
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+ Breakpoints
| Breakpoint 1 | chr5:178799281-178807738 | Breakpoint 2 | chr5:178861581-178862360 | |||||||||||||
| Definition method | Default informatic definition | |||||||||||||||
| Mechanism of origin |
NA
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| Flexibility | 11.81 | GC content | 0.26 | Stability | 1.69 |
| Position SD1 | Size (bp) | Position SD2 | Size (bp) | Identity | Relative orientation |
| chr5:178802777-178811616 | 8,840 | chr5:178857371-178867555 | 10,185 | 0.926 | Inverted |
+ 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
- 2015-02-23 10:14:33
| Breakpoint 1 | chr5:178799281-178807738 | Breakpoint 2 | chr5:178861581-178862360 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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Contact us at invfestdb@uab.cat
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