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furthermore, micra was run with the h37rv genome in place of the k12-dh10b genome as a reference. micra identified a total of 14 variants in the whole set of reads (table 2), of which six were detected by micra when the whole k12-dh10b genome was used as reference sequence. five snvs with frequencies between 81.74% and 99.94% in the whole set were found with micra when h37rv was used as reference sequence. three of them were snvs in an is6 transposase (locus: ecdh10b_0071) at a position with only a t in the h37rv sequence, resulting in a lysine to arginine change at position ecdh10b_0071:216,816(99.94% frequency of k to r), resulting in a lysine to arginine change at position ecdh10b_0071:216,816(99.94% frequency of k to r), resulting in a lysine to arginine change at position ecdh10b_0071:216,816 (99.94% frequency of k to r).
the simulated reads were used to estimate, for each mutation rate, the minimum number of reads and minimum base coverage required to achieve a base-calling error rate of 1% and a coverage lower than 50%. with no simulated e. coli pe reads, the base calling error rate is equal to 10 times the mutation rate (fig. 3). this gives an estimation of the expected error rate obtained with a complete e. coli genome sequencing project, whatever the sequencing method. a typical sequencing project consists in a limited number of amplicons or single chromosomes, thus the simulated e. coli reads are used to evaluate the noise level in the estimation of mutation rates. with the artificial mutation rates ranging from 0 to 10×10-4 per nucleotide, a mean sequencing depth of 40× decreases to 48, 66, and 84 when error rates of 1%, 10%, and 100% are targeted respectively. moreover, a sequencing depth of 30× increases to 44, 64, and 84 when error rates of 1%, 10%, and 100% are targeted, respectively.
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