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Table 3 Amplicon PrimerBLAST results

From: A high-throughput Sanger strategy for human mitochondrial genome sequencing

Amplicon number Number of nuclear genome matches Nuclear genome location GenBank accession number Priming region similarity (forward; reverse) Size difference from mtDNA target (in bp) Sequence similarity to rCRS
1 1 Chr 11 (9510471–9507925) NT_009237.18 76.2%; 76.2% 170 < 60%
2 1 Chr 6 (53426379–53424135) NT_025741.15 84.2%; 78.9% 118 < 60%
3 1 Chr 1 (43791–46082) NT_004350.19 100%; 100% 1 98.47%
4 2 Chr 1 (45818–48327) NT_004350.19 95.5%; 100% 1 98.57%
Chr 5 (7704044–7701575) NT_034772.6 95.5%; 90.9% 1 88.53%
5 2 Chr 7 (6847950–6850445) NT_033968.6 84.0%; 88.9% 7 75.16%
Chr 2 (10717704–10720523) NT_022135.16 80.0%; 88.9% 331 63.40%
6 2 Chr 5 (42577018–42574300) NT_034772.6 95.5%; 100% 0 94.02%
Chr 5 (7699358–7696640) NT_034772.6 90.5%; 90.0% 0 88.97%
7 4 Chr 5 (2218206–2220412) NT_034772.6 95.2%; 90.0% 1 87.27%
Chr 5 (2218173–2220412) NT_034772.6 81.0%; 90.0% 32 87.19%
Chr 17 (13111672–13109937) NT_010718.16 80.0%; 85.0% 453 < 60%
Chr 7 (5831689–5829543) NT_033968.6 81.0%; 75.0% 41 < 60%
  1. CodR amplification primer pairs were queried against the reference assembly of the complete human genome using PrimerBLAST [24], and results which met specific similarity criteria were noted. For these thirteen regions of the nuclear genome which are potentially amplifiable using the codR PCR primer pairs listed in Table 1, the nuclear genome sequence was aligned to the rCRS [22] to determine a percentage sequence similarity. The two Chromosome 5 matches listed for Amplicon 7 represent slightly different primer binding sites within the same portion of the chromosome.