Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 3,512,376 (T)5→4 coding (48/522 nt) aroK ← shikimate kinase AroK

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,512,3720T.98.6% 324.9 / ‑2.1 73coding (52/522 nt)aroKshikimate kinase AroK
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base . (29/43);  total (30/43)
Fisher's exact test for biased strand distribution p-value = 4.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.88e-01

CATCAGCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAA  >  NZ_CP009273/3512285‑3512453
                                                                                       |                                                                                 
caTCAGCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCttt                                                                                 >  2:22000/1‑90 (MQ=255)
   cAGCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCttttcc                                                                              <  1:1101514/90‑3 (MQ=255)
     gCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCttttccgg                                                                            <  2:218902/90‑5 (MQ=255)
     gCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCttttccgg                                                                            >  1:853269/1‑86 (MQ=255)
     gCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCttttccgg                                                                            >  1:136345/1‑86 (MQ=255)
     gCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCttttccgg                                                                            >  1:1433662/1‑86 (MQ=255)
     gCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCttttccgg                                                                            >  2:726093/1‑86 (MQ=255)
     gCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCttttccgg                                                                            >  1:655225/1‑86 (MQ=255)
     gCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCttttccgg                                                                            >  1:566313/1‑86 (MQ=255)
     gCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCttttccgg                                                                            >  1:378313/1‑86 (MQ=255)
     gCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCTTTTTCCg                                                                            >  2:305277/1‑90 (MQ=255)
      cTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGc                                                                          <  2:721125/90‑1 (MQ=255)
       tCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCCTATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCa                                                                         <  1:1096518/90‑1 (MQ=255)
       tCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCa                                                                         <  2:1330711/90‑1 (MQ=255)
       tCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCa                                                                         <  2:1308528/90‑1 (MQ=255)
       tCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCa                                                                         <  2:378313/90‑1 (MQ=255)
       tCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCa                                                                         <  2:860342/90‑1 (MQ=255)
          ggTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCAccc                                                                      >  2:1233867/1‑90 (MQ=255)
          ggTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCAccc                                                                      >  2:901874/1‑90 (MQ=255)
          ggTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCAccc                                                                      >  1:798132/1‑90 (MQ=255)
            ttCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCAt                                                                    <  2:1368472/90‑1 (MQ=255)
            ttCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCAt                                                                    <  1:987370/90‑1 (MQ=255)
               gTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAgg                                                                 >  1:384338/1‑90 (MQ=255)
               gTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAgg                                                                 >  2:1018568/1‑90 (MQ=255)
                  tctcAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGccc                                                              <  2:188740/90‑1 (MQ=255)
                   ctcAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCa                                                             <  1:784873/90‑1 (MQ=255)
                    tcAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCaa                                                            <  1:493916/90‑1 (MQ=255)
                     cAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAAc                                                           >  2:717502/1‑90 (MQ=255)
                     cAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAAc                                                           >  2:682002/1‑90 (MQ=255)
                      aaTCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAAcc                                                          <  2:1246885/90‑1 (MQ=255)
                          tctTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGc                                                                <  2:1260066/80‑1 (MQ=255)
                          tctTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGc                                                                >  1:1260066/1‑80 (MQ=255)
                          tctTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCa                                                             >  2:67310/1‑83 (MQ=255)
                          tctTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCa                                                             <  1:67310/83‑1 (MQ=255)
                          tctTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGaa                                                      <  2:460054/90‑1 (MQ=255)
                          tctTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGaa                                                      <  2:949836/90‑1 (MQ=255)
                          tctTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGaa                                                      <  1:579926/90‑1 (MQ=255)
                           ctTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGaaa                                                     <  2:585674/90‑1 (MQ=255)
                           ctTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGaaa                                                     <  2:1386315/90‑1 (MQ=255)
                           ctTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGaaa                                                     <  2:853269/90‑1 (MQ=255)
                                   gAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCa                                                                         >  2:243936/1‑62 (MQ=255)
                                   gAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCa                                                                         <  1:243936/62‑1 (MQ=255)
                                   gAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGc                                             >  1:555299/1‑90 (MQ=255)
                                   gAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGc                                             >  2:916371/1‑90 (MQ=255)
                                        gTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGccc                                                              >  2:993183/1‑68 (MQ=255)
                                        gTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGccc                                                              <  1:993183/68‑1 (MQ=255)
                                          aaaaTTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTtctc                                      <  2:437087/90‑1 (MQ=255)
                                                 cATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCAtt                               <  1:269086/90‑1 (MQ=255)
                                                  atatTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCAc                                                                        >  1:830616/1‑48 (MQ=255)
                                                  atatTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCAc                                                                        <  2:830616/48‑1 (MQ=255)
                                                  atatTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCAttt                              >  2:707686/1‑90 (MQ=255)
                                                      tGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTc                          <  2:1096583/90‑1 (MQ=255)
                                                      tGAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTc                          <  1:175231/90‑1 (MQ=255)
                                                       gAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGccc                                                              >  2:1355202/1‑53 (MQ=255)
                                                       gAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGccc                                                              <  1:1355202/53‑1 (MQ=255)
                                                       gAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCg                         >  2:1335795/1‑90 (MQ=255)
                                                       gAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCg                         >  2:513919/1‑90 (MQ=255)
                                                       gAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCg                         >  1:23480/1‑90 (MQ=255)
                                                       gAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCg                         >  2:151317/1‑90 (MQ=255)
                                                       gAGTTGTTGAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCg                         >  2:909335/1‑90 (MQ=255)
                                                          ttgttgAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGta                      <  2:900580/90‑1 (MQ=255)
                                                          ttgttgAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGta                      <  2:902085/90‑1 (MQ=255)
                                                          ttgttgAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGta                      <  1:1061151/90‑1 (MQ=255)
                                                          ttgttgAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGta                      <  1:726093/90‑1 (MQ=255)
                                                          ttgttgAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGta                      <  2:682963/90‑1 (MQ=255)
                                                          ttgttgAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGta                      <  2:1148575/90‑1 (MQ=255)
                                                          ttgttgAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGta                      <  1:847820/90‑1 (MQ=255)
                                                          ttgttgAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGta                      <  2:1433662/90‑1 (MQ=255)
                                                          ttgttgAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGta                      <  1:862723/90‑1 (MQ=255)
                                                          ttgttgAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGta                      <  1:717502/90‑1 (MQ=255)
                                                            gttgAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGtact                    >  2:272863/1‑90 (MQ=255)
                                                               gAGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTactact                 <  2:67898/90‑1 (MQ=255)
                                                                aGCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTActacta                <  2:136345/90‑1 (MQ=255)
                                                                 gCTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTaa               >  1:97126/1‑90 (MQ=255)
                                                                  cTAACTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAg              <  1:916371/90‑1 (MQ=255)
                                                                      cTGGCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTa          >  2:1212909/1‑90 (MQ=255)
                                                                        ggCGCCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTAtt        <  1:2511/90‑1 (MQ=255)
                                                                         gcgcCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTc       >  2:35943/1‑90 (MQ=255)
                                                                         gcgcCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATAATGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTc       >  2:1335344/1‑90 (MQ=255)
                                                                           gcCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGt     >  1:1304027/1‑90 (MQ=255)
                                                                           gcCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGt     >  1:1031223/1‑90 (MQ=255)
                                                                           gcCCAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGt     >  1:102750/1‑90 (MQ=255)
                                                                              cAATAGTGC‑TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTaa  <  1:272863/90‑1 (MQ=255)
                                                                                       |                                                                                 
CATCAGCTCCGGTTCGTTTCTCAATCTCTTGATCGGAATCGTAAAATTCCATATTGAGTTGTTGAGCTAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAA  >  NZ_CP009273/3512285‑3512453

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑