| Accession | HsInv0448 | Region of the inversion | chr2:110341747-110642161 |
| Status | False | Prediction type | Simple |
| Estimated Inversion Size | 283,907 bp | Supporting predictions | 1 |
| Inverted allele frequency | NA | Mechanism of origin | NA |
| Functional effect | Breaks one gene | Breakpoint 1 | chr2:110341747-110360143 |
| Ancestral orientation | NA | Breakpoint 2 | chr2:110627541-110642161 |
| Comments | False inversion prediction caused by incorrect paired-end mapping due to a 150-kb sequencing gap in HG18 that has been filled in HG19
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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 | chr2:110341747-110360143 | Breakpoint 2 | chr2:110627541-110642161 | ||||||||||||||||||||
| D/C Score | -5.85 | Disc. Support Prob. | 0 | ||||||||||||||||||||
| Support | 15 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 a sequencing gap in the HG18 genome. | ||||||||||||||||||||||
+ 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 a 150 kb gap in HG18 genome (chr2:110348651-110498718) has been filled with 73 kb of sequence in HG19 that expands existing SDs. This new sequence provides additional concordant mappings for the fosmid ends with almost the same or higher identity than the discordant mappings supporting the inversion prediction in HG18. Analysis of AC226803.2 fosmid sequence indicates that the whole fosmid maps continuously and with high identity to HG19. |
+ Frequency
No frequency studied
+ Breakpoints
| Breakpoint 1 | chr2:110341747-110360143 | Breakpoint 2 | chr2:110627541-110642161 | |||||||||||||
| Definition method | Default informatic definition | |||||||||||||||
| Mechanism of origin |
NA
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| Flexibility | 5.17 | GC content | 0.29 | Stability | 0.99 |
| Position SD1 | Size (bp) | Position SD2 | Size (bp) | Identity | Relative orientation |
| chr2:110343049-110348650 | 5,602 | chr2:110627783-110633379 | 5,597 | 0.998 | 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
| Gene position | chr2:110595032-110665189 |
| Mechanism | Breaks one gene |
+ Inversion phenotypical effects
Not defined
+ Report history
- 2015-02-23 10:14:31
| Breakpoint 1 | chr2:110341747-110360143 | Breakpoint 2 | chr2:110627541-110642161 |
| Assembly | hg18 | ||
| Definition method | Default informatic definition | ||
