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This second analysis sought to establish during which bins the observed proportion mismatched the expected proportion.
The proportion of mismatch probes with intensities greater than 2, 4, or 8 times the median for all mismatch probes on the same array.
The remaining eleven inbred lines, including four CMLs and all seven lines from EIAR, showed higher proportion of mismatch for two or more seed sources.
For each dataset, we calculated a global average proportion of mismatching reads, and used the binomial test to identify stop codon nucleotides whose individual proportion of mismatches significantly deviated from the corresponding global average.
The error rate was calculated as the proportion of mismatches between duplicated, single-locus genotypes.
Another platform-specific characteristic observed in this study was the proportion of mismatches within a non-perfectly mapped read.
An alternate explanation for a low but elevated proportion of mismatches is RNA editing, the conversion of one nucleotide to another in an mRNA.
When expressed in this manner, the proportion of mismatches per length of non-perfectly matched reads is 0.5 for the MiSeq versus 0.4 for the PGM.
The empirical frequency of Watson Crick base pairs is 80%, with the remaining base pairs consisting primarily of wobble base pairs (13%) and a smaller proportion of mismatches (7%).
The distance-matrix methods rely on the "genetic distances" between the sequences being investigated where the distance is calculated from the proportion of mismatches in a multiple sequence alignment.
In these alignments, the proportion of mismatches was highest at the ends of these alignments where there are typically lower numbers of sequencing reads (Fig. 3).> -wrap-foot> Summary of BLASTN searches of the transcriptome using published sequences from five protein-coding genes as queries.
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