Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	478,730	A→G	100%	L377P (CTC→CCC)	acrB ←	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	478,730	0	A	G	100.0%	156.8 / ‑6.7	45	L377P (CTC→CCC)	acrB	multidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (21/23);  minor base C (1/0);  total (22/23)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGAGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGACGGGAAGAACGGTTCCATCTTCGCCAGTTCAGCACGGATTGCC  >  CP009273/478470‑478948                                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                           cAGTAGAACAGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGAGGCAAACCTTCTTCCGCCATAACACCCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTTTCAGCGTGTATATCGAAAAGACAAAGAAGGCACCGACANCACAGGTCCCGCCAAACaccaccct                                                                                                                                                                                                               >  2:438448/1‑272 (MQ=25)                                       gccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCCGCAAACCTTCTTCCGCCATAACCCGCTCAACGCTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGCCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAAAACCACCGGTACAGCAATGGGCTTACTCAAAGCNGCGCGGAAATTCta                                                                                                                                                                        >  2:499687/1‑274 (MQ=38)                                                aCCATCGCGAGACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGAGGCAAACCTTCTTCCNCCATAACANGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCATCGTCGCGCGGAAGTTCTGCAGGAACa                                                                                                                                                                <  1:438454/274‑1 (MQ=255)                                                      gcgATACCGACCATAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAACACGCTCAANGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGCTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACAt                                                                                                                                                         <  1:499696/275‑1 (MQ=255)                                                                                                      gCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGGCGGAATCAACGTcgc                                                                                                                                                                                    >  2:548652/1‑200 (MQ=255)                                                                                                          cttTTGGCGGCAAACCTTCTTCCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCgg                                                                                                                                                                                <  1:548663/200‑1 (MQ=255)                                                                                                                              tcCGCCATCACACGCTGAACGTTTTCTACTACAACGATGGCGTCATCCAGCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCNTGTTTATCGAGAAGCCAAATGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCTGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACGACTTCGTGAATAGAGATTTTCACGAACg                                                                                  <  1:510788/274‑1 (MQ=255)                                                                                                                                   cATAACCCGCTCAACGTTTTCTACCACAACTATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTTTTTATCGAGAAGCCAATGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtgg                                                                            <  1:421750/275‑1 (MQ=255)                                                                                                                                   cATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCACGAACATTGTTAGCGTGTTTATCGAGAAGACAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGAAGAACGCTCCGACCAGCGTTTTAAGCACTTCGTTGATAGCGATTTTCACGACAGACgtgg                                                                            >  2:611646/1‑275 (MQ=38)                                                                                                                                                              aaCGATGGCGTCATCCACCAACAGGCCGATGGCTAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATaccac                                                                                                                                                                                                                  >  2:589581/1‑114 (MQ=255)                                                                                                                                                                  aTGGCGTCATCCACCAACAGGCCGATGGCTAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGt                                                                                                                                                                                                              <  1:589592/114‑1 (MQ=255)                                                                                                                                                                        tCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCgg                                                                                                                                                                                >  1:442395/1‑138 (MQ=255)                                                                                                                                                                            ccaccaACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGt                                                                                                                                                                            <  2:442389/138‑1 (MQ=255)                                                                                                                                                                                 aaCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTGTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGTTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAgg                                                                                                                                         >  1:42019/1‑168 (MQ=255)                                                                                                                                                                                     ggCCGATGGCGAGAACCAGCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGTTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGgatga                                                                                                                                     <  2:42019/168‑1 (MQ=255)                                                                                                                                                                                          aTGGCGAGCACCATCCCGAACATTGTTATCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCNCGGAAGTTCTTTAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGACGGGAAGAACGGTTCCATCTTCGc                     <  1:611657/275‑1 (MQ=255)                                                                                                                                                                                          aTGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATa                                                                                                                                                                                                                      >  2:615020/1‑82 (MQ=255)                                                                                                                                                                                              cGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATaccac                                                                                                                                                                                                                  <  1:615031/82‑1 (MQ=255)                                                                                                                                                                                                aGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATa                                                                                                                                                                                                                      >  1:567912/1‑76 (MQ=255)                                                                                                                                                                                                  cACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGa                                                                                                                                                                   >  2:609277/1‑125 (MQ=255)                                                                                                                                                                                                    ccATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATacaac                                                                                                                                                                                                                  <  2:567901/76‑1 (MQ=255)                                                                                                                                                                                                      aTCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAg                                                                                                                                                               <  1:609288/125‑1 (MQ=255)                                                                                                                                                                                                          cGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATa                                                                                                                                                                                                                      >  1:24682/1‑66 (MQ=255)                                                                                                                                                                                                              cATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATaccac                                                                                                                                                                                                                  <  2:24682/66‑1 (MQ=255)                                                                                                                                                                                                               aTTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCa                                                                                                                                                                                           >  2:494844/1‑88 (MQ=255)                                                                                                                                                                                                                 tGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCAGGGCAATACCACCGGTACGGCAATGGTCg                                                                                                                                                                                                 >  1:197944/1‑80 (MQ=255)                                                                                                                                                                                                                   ttAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGt                                                                                                                                                                                       <  1:494852/88‑1 (MQ=255)                                                                                                                                                                                                                   ttAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAgg                                                                                                                                                                    >  1:358190/1‑107 (MQ=255)                                                                                                                                                                                                                     aGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATa                                                                                                                                                                                                                      >  1:146643/1‑55 (MQ=255)                                                                                                                                                                                                                     aGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAg                                                                                                                                                                     >  1:539135/1‑104 (MQ=255)                                                                                                                                                                                                                     aGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGaa                                                                                                                                                                  >  2:576183/1‑107 (MQ=255)                                                                                                                                                                                                                     aGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCAGGGCAATACCACCGGTACGGCAATGGTCGGAAt                                                                                                                                                                                             <  2:197940/80‑1 (MQ=255)                                                                                                                                                                                                                       cGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACa                                                                                                                                                                <  2:358185/107‑1 (MQ=255)                                                                                                                                                                                                                         tgtTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATaccac                                                                                                                                                                                                                  <  2:146640/55‑1 (MQ=255)                                                                                                                                                                                                                         tgtTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAAc                                                                                                                                                                 <  2:539124/104‑1 (MQ=255)                                                                                                                                                                                                                         tgtTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGa                                                                                                                                                              <  1:576194/107‑1 (MQ=255)                                                                                                                                                                                                                         tgtTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGtttt                                                                                                                  >  1:418410/1‑151 (MQ=255)                                                                                                                                                                                                                             tATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAAcc                                                                                                              <  2:418405/151‑1 (MQ=255)                                                                                                                                                                                                                             tATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACg                                                                                      >  2:625022/1‑175 (MQ=255)                                                                                                                                                                                                                               tCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGGGCAAt                                                                                                                                                                                                                       <  2:144401/44‑1 (MQ=255)                                                                                                                                                                                                                                                gcAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAgg                                                                                                                                                                    >  2:252420/1‑78 (MQ=255)                                                                                                                                                                                                                                                 cAAGGACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGAc                                                                                                                           >  1:546188/1‑118 (MQ=255)                                                                                                                                                                                                                                                    ggACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACa                                                                                                                                                                <  1:252424/78‑1 (MQ=255)                                                                                                                                                                                                                                                     gACGGCAAAGGTCCCGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGc                                                                                                                       <  2:546177/118‑1 (MQ=255)                                                                                                                                                                                                                                                                  ccGGGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGACGGGAAGAACGGTTCCATCTTCGCCAGTTCAGCACGGATTGcc  >  2:111283/1‑222 (MQ=255)                                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                           CAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCCGAGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGACGGGAAGAACGGTTCCATCTTCGCCAGTTCAGCACGGATTGCC  >  CP009273/478470‑478948

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑