| Accession | HsInv0672 | Region of the inversion | chr2:85395413-85426637 |
| Status | False | Prediction type | Simple |
| Estimated Inversion Size | 28,701 bp | Supporting predictions | 3 |
| Inverted allele frequency | NA | Mechanism of origin | NA |
| Functional effect | Breaks one gene | Breakpoint 1 | chr2:85395413-85398211 |
| Ancestral orientation | NA | Breakpoint 2 | chr2:85424386-85426637 |
| 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
| Description | Paired-end mapping analysis of the J. Craig Venter genome (HuRef) | ||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr2:85395953-85397671 | Breakpoint 2 | chr2:85424379-85425944 | ||||
| Individuals |
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| Description | Next generation sequencing and analysis by paired-end mapping of a Korean individual genome | ||||||||||||||||||
| Method | Paired-end mapping (PEM) | ||||||||||||||||||
| Name | |||||||
| Breakpoint 1 | chr2:85396503-85396623 | Breakpoint 2 | chr2:85424328-85424459 | ||||
| Individuals |
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| Comments | Both predicted breakpoints are located in a region of sequence variation within SDs and discordant PEM pattern is probably caused by incorrect mapping of one end sequence. | ||||||
- 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 | chr2:85379401-85409934 | Breakpoint 2 | chr2:85424386-85435097 | ||||||||||||||||||||
| D/C Score | -3.33 | Disc. Support Prob. | 0.00755 | ||||||||||||||||||||
| Support | 3 probes  | ||||||||||||||||||||||
| Individuals |
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| Comments | Below the threshold of the Discordant/Concordant (D/C) ratio score. Discordant PEM pattern caused by incorrect mapping of one end of all fosmids due to sequence variation within SDs. | ||||||||||||||||||||||
+ Validation and genotyping
-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
No frequency studied
+ Breakpoints
| Breakpoint 1 | chr2:85395413-85398211 | Breakpoint 2 | chr2:85424386-85426637 | |||||||||||||
| Definition method | Default informatic definition | |||||||||||||||
| Mechanism of origin |
NA
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| Flexibility | 10.24 | GC content | 0.5 | Stability | 2.01 |
| Position SD1 | Size (bp) | Position SD2 | Size (bp) | Identity | Relative orientation |
| chr2:85394273-85398062 | 3,790 | chr2:85422969-85425835 | 2,867 | 0.948 | 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
- RETSAT
| Gene position | chr2:85422588-85435332 |
| Mechanism | Breaks one gene |
+ Inversion phenotypical effects
Not defined
+ Report history
- 2015-02-23 10:14:30
| Breakpoint 1 | chr2:85395413-85398211 | Breakpoint 2 | chr2:85424386-85426637 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:30
| Breakpoint 1 | chr2:85379401-85409934 | Breakpoint 2 | chr2:85424386-85435097 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:30
| Breakpoint 1 | chr2:85379401-85409934 | Breakpoint 2 | chr2:85423859-85435097 |
| Assembly | hg18 | ||
| Description | Breakpoints not refined due to lack of overlap of predictions in at least one breakpoint. Breakpoints calculated without considering unreliable predictions | ||
| Definition method | Default informatic definition | ||
- 2015-02-23 10:14:30
| Breakpoint 1 | chr2:85395413-85398211 | Breakpoint 2 | chr2:85424386-85426637 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
