FIG 3.

Base calling differences for the Illumina MiSeq and ABI 3730xl Sanger sequencing methods. A change matrix displays the frequency of nucleotides detected by Sanger (rows) and MiSeq (columns) sequencing. Overall, 832 clinical samples and 11 technical replicate samples were successfully sequenced by both methods. A total of 2,466 mismatches were identified in 366,705 called bases in these samples. Concordant base calls are highlighted in green, partially discordant base calls (mixed bases detected by one method but not the other) are highlighted in yellow, and entirely discordant base calls are highlighted in red. Differences in mixture detection or calling accounted for >95% of all discordant bases. Rows for B, D, H, and V are not shown for Sanger base calls, as the RECall software does not call three-base mixtures.