| Accession | HsInv0284 | Region of the inversion | chr6:142229154-142261544 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 32,390 bp | Supporting predictions | 2 |
| Inverted allele frequency | 0.0556 | Mechanism of origin | NHEJ |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr6:142229154-142229155 |
| Ancestral orientation | NA | Breakpoint 2 | chr6:142261543-142261544 |
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Human Polymorphic Inversion DataBase
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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 | chr6:142229157-142229157 | Breakpoint 2 | chr6:142261539-142261539 |
| Individuals | 149 out of 2504 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 | chr6:142217314-142235320 | Breakpoint 2 | chr6:142245839-142281870 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.97665 | ||||||||||||||||||||
| Support | 6 probes | ||||||||||||||||||||||
| Individuals |
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+ Validation and genotyping
| 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 | Sequence analysis |
| Status | Validated |
| Comment | Simple inversion validated by sequence analysis of PacBio long reads from fosmids |
-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
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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) (Martinez-Fundichely et al. 2014 (in preparation)) | 4 | 1 | 0.8750 | 0.1250 | > 0.5 |
| Africa (AFR)
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Africa (AFR) summary | 4 | 1 | 0.8750 | 0.1250 | > 0.5 |
|---|
+ 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) (Martinez-Fundichely et al. 2014 (in preparation)) | 2 | 0 | 1.0000 | 0.0000 | NA |
| Europe (EUR)
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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
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Han Chinese in Beijing, China (CHB) (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 0 | 1.0000 | 0.0000 | NA |
| Japanese
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Japanese in Tokyo, Japan (JPT) (Martinez-Fundichely et al. 2014 (in preparation)) | 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 |
|---|
+ Unknown
| Population | Sample and Study | Independent individuals | Inverted alleles | Standard frequency | Inverted frequency | HWE p-value |
|---|---|---|---|---|---|---|
| Unknown
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Unknown (Martinez-Fundichely et al. 2014 (in preparation)) | 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 | chr6:142229154-142229155 | Breakpoint 2 | chr6:142261543-142261544 | ||
| 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
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| Flexibility | 11.59 | GC content | 0.28 | Stability | 1.73 |
| Comments |
Inversion generated probably by non-homologous end joining (NHEJ) with clean and 2-bp staggered breaks mediated by 14bp microhomology |
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+ 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 | chr6:142224157-142234157 | Breakpoint 2 | chr6:142256539-142266539 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-03-12 09:01:19
| Breakpoint 1 | chr6:142229154-142229155 | Breakpoint 2 | chr6:142261543-142261544 |
| 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 10:14:34
| Breakpoint 1 | chr6:142217314-142235320 | Breakpoint 2 | chr6:142245839-142281870 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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Contact us at invfestdb@uab.cat
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.