Table S1 Mitochondrial position and average sequence coverage for 87 mitochondrial SNPs identified in our specimen, DZ762, compared to the R.    norvegicus reference genome.

Table S2 Calculation of general error rate and biases in error rates.

Fig. S1 Flow diagram of data cleaning and alignment from raw reads to mapped reads.

Fig. S2 (A) Mapping of paired reads. (B) Distance between reads mapped to the same chromosome.

Fig. S3 Broad scale coverage of nuclear genome calculated for 10-kb windows of the chromosome.

Fig. S4 Correlation between coverage of the mitochondrial genomes for the two libraries.

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