Three alleles of qSW5/GW5 gene were distinguished by length of deletion at the qSW5/GW5 locus (Yan et al. 2011): Kasalath-allele (no deletion), indica II-allele (950 bp deletion), and Nipponbare-allele (1,212 bp deletion).
Four deletion rates were tested: equal to the mutation rate, 10 or 100 times slower than the mutation rate, and equal to 0 (no deletion).
We do not observe a significant increase in the false positive rate because the probability of a no deletion site is only reduced slightly.
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However, some wild-type A. oryzae strains have no deletion in the ustR upstream region and are in this respect similar to A. flavus (our unpublished data).
No deletion of the cagA, cagE and cagT genes, involved in benign cases, was observed [29].
The total alignment included 45 substitutions, of which 38 were affected by transitions and 7 by transversions, but no deletion and insertion were observed.
No deletion or amplification at the breakpoint was observed in the five t-AML, nor in the two p-AML cases with rearranged MLL.
We grouped these deletion patterns into 10 different haplotypes where haplotype H1 designates no deletion on 1p, H2 H9 partial 1p deletion patterns, and H10, complete loss of 1p (Figure 1A).
No deletion of Bn.FAE1-C3 was designated haplotype C3-H0.
