| Accession | HsInv0092 | Region of the inversion | chr6:130889879-130893988 |
| Status | Validated | Prediction type | Simple |
| Estimated Inversion Size | 4,110 bp | Supporting predictions | 5 |
| Inverted allele frequency | 0.2222 | Mechanism of origin | NHEJ |
| Functional effect | Intergenic breakpoints | Breakpoint 1 | chr6:130889879-130889879 |
| Ancestral orientation | NA | Breakpoint 2 | chr6:130893988-130893988 |
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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 | chr6:130889891-130889891 | Breakpoint 2 | chr6:130894011-130894011 |
| Individuals | 681 out of 2504 individuals
 | ||
| Description | Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1) | ||||||||||||||
| Method | Long-read sequencing | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr6:130889878-130889878 | Breakpoint 2 | chr6:130893988-130893988 | ||||
| Individuals |
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| Description | Next generation sequencing and analysis by paired-end mapping of an individual genome of African origin | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr6:130889860-130889877 | Breakpoint 2 | chr6:130893985-130894002 | ||||
| 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 | chr6:130892316-130892316 | Breakpoint 2 | chr6:130894765-130894765 | ||||||
| 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 | chr6:130851649-130891565 | Breakpoint 2 | chr6:130893244-130928639 | ||||||||||||||||||||
| D/C Score | NA | Disc. Support Prob. | 0.99251 | ||||||||||||||||||||
| Support | 4 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 Oxford Nanopore Minion long reads from long-range PCR amplicons, PacBio long reads from CHM1 genome |
| Description | Identification and resolution of sequence gaps and structural variants in the euchromatic regions of the reference human assembly through single-molecule, real-time (SMRT) DNA sequencing of an haploid human genome (CHM1) | ||||
| Method | Sequence analysis |
| Status | Validated |
| Comment | Inversion validated by analysis of CH17-330F8 BAC sequence (AC255402) obtained with the Illumina Nextera system |
| 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 6 STD/STD - 2 STD/INV - 1 INV/INV - 1 NA |
- 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 | 4 | 0.5000 | 0.5000 | > 0.5 |
| Africa (AFR)
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Africa (AFR) summary | 4 | 4 | 0.5000 | 0.5000 | > 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
|
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
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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
|
Unknown (Martinez-Fundichely et al. 2014 (in preparation)) | 1 | 0 | 1.0000 | 0.0000 | NA |
| Unknown
|
Unknown summary | 1 | 0 | 1.0000 | 0.0000 | NA |
|---|
+ Breakpoints
| Breakpoint 1 | chr6:130889879-130889879 | Breakpoint 2 | chr6:130893988-130893988 | ||
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||||
| Description | Breakpoints defined by sequencing of inverted PCR fragments | ||||
| Definition method | Manual curation | ||||
| Mechanism of origin |
NHEJ
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| Flexibility | 10.79 | GC content | 0.44 | Stability | 1.94 |
| Comments |
Inversion generated probably by non-homologous end joining (NHEJ) with no microhomology and breakpoints can be located within one single base |
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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
- 2017-09-29 00:00:00
| Breakpoint 1 | chr6:130885506-130891565 | Breakpoint 2 | chr6:130893244-130898988 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2017-09-18 00:00:00
| Breakpoint 1 | chr6:130885506-130891565 | Breakpoint 2 | chr6:130893244-130899011 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-03-11 16:55:16
| Breakpoint 1 | chr6:130889879-130889879 | Breakpoint 2 | chr6:130893988-130893988 |
| Study | Martinez-Fundichely et al. 2014 (in preparation) | ||
| Assembly | hg18 | ||
| Description | Breakpoints defined by sequencing of inverted PCR fragments | ||
| Definition method | Manual curation | ||
- 2015-02-23 10:14:34
| Breakpoint 1 | chr6:130885506-130891565 | Breakpoint 2 | chr6:130893244-130899546 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
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Contact us at invfestdb@uab.cat
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