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This suggests that the SNP analysis may define a common haplotype representing many inversion chromosomes, but such an analysis may misclassify some alleles and thus underestimate the true inversion frequency.
Our estimate is in the style of the IEBP estimate for the true inversion distance for a single chromosome due to Wang (2001) (see also Wang and Warnow 2001), in that it does not require computing an edit distance, but only a simple count of shared gene adjacencies [or, equivalently, breakpoints, as in the seminal work of Sankoff and Blanchette (1998, 1999)] and chromosome endpoints.
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When a whole, otherwise independent, block (scaffold or chromosome) was classed as inverted, this was counted in the analysis as a true inversion if a different orientation was recovered for two or more species (example shown in Figure 3b for chromosome 11 in zebra finch).
Sensitivity for searching for the true ultramicro inversions in simulation in the AT-exclusive condition was less than that in the initial condition and, as well as the initial condition, increased with increasing inversion size from 0.218 for 5 bp inversion to 0.768 for 50 bp inversion.
Although there probably are true inversions and transpositions among the accessions we resequenced, it remains a challenge to reliably identify them using paired-end reads.
Given the number of inversions already identified, it is conceivable that this parsimony approach has underestimated the true number of inversion events that occurred during cupressophyte diversification.
Over the next year or two, the true extent of inversion variants in the human genome will be revealed.
However, the true extent of inversions or other structural rearrangements are unknown between all of the crosses analysed.
This reflects the true state of criminal inversion of society, where the people who act courageously to expose crime are vilified and attacked by the criminals because it is they who own and control the instruments of justice and law.
The method updates an initial Q guess to the true Q distribution through inversion.
Using GRAPPA, all rearrangements were inferred as inversions, but the total number of inversion events estimated by GRAPPA may be greater than the true (but unknown) mixture of inversions and transpositions because one transposition could result in the same change in gene order as two or three inversions.
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