Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	465,464	T→C	S380P (TCG→CCG)	mdlA →	SmdA family multidrug ABC transporter permease/ATP‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	465,464	0	T	C	100.0%	271.9 / NA	72	S380P (TCG→CCG)	mdlA	SmdA family multidrug ABC transporter permease/ATP‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (30/42);  total (30/42)

CGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTG  >  NZ_CP009273/465378‑465549                                                                                       |                                                                                      cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc                                                                                    <  1:1077719/90‑1 (MQ=255) cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc                                                                                    <  2:744725/90‑1 (MQ=255) cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc                                                                                    >  1:3008170/1‑90 (MQ=255) cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc                                                                                    >  1:744725/1‑90 (MQ=255) cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc                                                                                    >  1:1639654/1‑90 (MQ=255)   cTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTc                                                                                  <  2:2265544/90‑1 (MQ=255)   cTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTc                                                                                  >  1:1748435/1‑90 (MQ=255)     ggAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCAt                                                                                >  1:1929749/1‑90 (MQ=255)               aaTTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCAt                                                                      >  1:1932203/1‑90 (MQ=255)                   tCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGCCTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCg                                                                  <  1:1924910/90‑1 (MQ=255)                    cGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTc                                                                   >  1:164354/1‑88 (MQ=255)                    cGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTc                                                                   <  2:164354/88‑1 (MQ=255)                     gCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGAc                                                                >  1:1086601/1‑90 (MQ=255)                      cccTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACg                                                               <  1:2284068/90‑1 (MQ=255)                        cTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTc                                                             <  2:1675374/90‑1 (MQ=255)                            aaCCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCg                                                         <  1:1695099/90‑1 (MQ=255)                            aaCCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCg                                                         <  1:1695621/90‑1 (MQ=255)                             aCCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGa                                                        <  1:1854297/90‑1 (MQ=255)                              cccGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAg                                                       <  1:618326/90‑1 (MQ=255)                               ccGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAgg                                                      <  2:32032/90‑1 (MQ=255)                                  gTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAg                                                       >  1:2441103/1‑86 (MQ=255)                                  gTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAg                                                       <  2:2441103/86‑1 (MQ=255)                                        tGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAATGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTc                                             <  2:474905/90‑1 (MQ=255)                                        tGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTc                                             <  2:36421/90‑1 (MQ=255)                                        tGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTc                                             <  2:2580858/90‑1 (MQ=255)                                        tGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTc                                             <  1:523847/90‑1 (MQ=255)                                         gCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCg                                            <  2:1929749/90‑1 (MQ=255)                                           tGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCt                                          <  2:782738/90‑1 (MQ=255)                                            gggTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCtt                                         <  2:1639654/90‑1 (MQ=255)                                            gggTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCtt                                         >  1:1891264/1‑90 (MQ=255)                                            gggTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCtt                                         >  1:2576191/1‑90 (MQ=255)                                             ggTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCttt                                        <  1:2390879/90‑1 (MQ=255)                                             ggTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCttt                                        <  1:312805/90‑1 (MQ=255)                                             ggTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCttt                                        <  1:594466/90‑1 (MQ=255)                                              gTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTc                                       <  2:829060/90‑1 (MQ=255)                                              gTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTc                                       <  1:554512/90‑1 (MQ=255)                                                aTCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAt                                     <  2:2046811/90‑1 (MQ=255)                                                aTCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAt                                     >  2:674948/1‑90 (MQ=255)                                                aTCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAt                                     <  2:1532387/90‑1 (MQ=255)                                                aTCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAt                                     >  1:823459/1‑90 (MQ=255)                                                aTCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAt                                     >  1:1584766/1‑90 (MQ=255)                                                 tCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATg                                    >  1:2500754/1‑90 (MQ=255)                                                    gCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGata                                 >  2:1428371/1‑90 (MQ=255)                                                      gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTc                                                                   >  2:1254349/1‑54 (MQ=255)                                                      gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTc                                                                   <  1:1254349/54‑1 (MQ=255)                                                      gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCtt                                         <  2:6917/80‑1 (MQ=255)                                                      gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCtt                                         >  1:6917/1‑80 (MQ=255)                                                        gCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTc                                                             <  2:564079/58‑1 (MQ=255)                                                        gCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTc                                                             >  1:564079/1‑58 (MQ=255)                                                        gCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTcc                             <  1:2050483/90‑1 (MQ=255)                                                           gACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTc                                             >  1:2785128/1‑71 (MQ=255)                                                           gACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTc                                             <  2:2785128/71‑1 (MQ=255)                                                           gACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCctct                          >  1:2302284/1‑90 (MQ=255)                                                            aCTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTg                         >  1:1689981/1‑90 (MQ=255)                                                               ggTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACg                      <  2:3004318/90‑1 (MQ=255)                                                                gTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGa                     <  1:2571864/90‑1 (MQ=255)                                                                 ttCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAgggg                                                    <  1:2828569/58‑1 (MQ=255)                                                                 ttCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAgggg                                                    >  2:2828569/1‑58 (MQ=255)                                                                 ttCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGaa                    >  2:2072507/1‑90 (MQ=255)                                                                 ttCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGaa                    >  2:2793557/1‑90 (MQ=255)                                                                   ccGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGt                  >  1:997953/1‑90 (MQ=255)                                                                    cGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGtt                 <  2:1833293/90‑1 (MQ=255)                                                                      gCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTAc               <  1:2280679/90‑1 (MQ=255)                                                                       cAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACa              <  2:323861/90‑1 (MQ=255)                                                                       cAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACa              <  1:1517721/90‑1 (MQ=255)                                                                         aaaGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAAc            >  2:2930306/1‑90 (MQ=255)                                                                         aaaGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAAc            >  1:1352038/1‑90 (MQ=255)                                                                             tACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGa        <  1:710388/90‑1 (MQ=255)                                                                               cccTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATa      >  2:2225831/1‑90 (MQ=255)                                                                                ccTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAg     >  1:1494206/1‑90 (MQ=255)                                                                                 cTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGc    <  1:2873548/90‑1 (MQ=255)                                                                                 cTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGc    <  1:1070177/90‑1 (MQ=255)                                                                                  tgttgcCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCt   <  2:632528/90‑1 (MQ=255)                                                                                   gttgcCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTg  >  2:129648/1‑90 (MQ=255)                                                                                       |                                                                                      CGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTG  >  NZ_CP009273/465378‑465549

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑