Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,978,089 A→C 24.4% M288R (ATG→AGG)  yqeF ← short chain acyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,978,0890AC24.4% 84.5 / 4.5 50M288R (ATG→AGG) yqeFshort chain acyltransferase
Reads supporting (aligned to +/- strand):  ref base A (14/23);  new base C (11/2);  total (25/25)
Fisher's exact test for biased strand distribution p-value = 8.30e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACCCGCTGTCACAGAACC  >  CP009273/2977940‑2978237
                                                                                                                                                     |                                                                                                                                                    
tgacCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCCTACACCCGCGCAATTCCCa                                                                                                                                                      >  2:883352/1‑150 (MQ=255)
   cccGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCACACCCCCGCGCCATTCCCATc                                                                                                                                                    >  1:395963/1‑149 (MQ=255)
     cGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATAAACCCGCGCCACTCCCCTCCAt                                                                                                                                                 >  2:318360/1‑150 (MQ=255)
      gACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACAACGGCGCCAATCCCATCAATg                                                                                                                                                >  2:774961/1‑150 (MQ=255)
        cGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGcc                                                                                                                                              <  1:426548/150‑1 (MQ=255)
                ccACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTac                                                                                                                                      <  2:715765/150‑1 (MQ=255)
                     cAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGCGCCATTCCCATCAATGCCGGATCTTCACCaa                                                                                                                                 >  2:401021/1‑150 (MQ=255)
                           tCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCCTACACCCGCGCAATTCCCCTCAATGCCGGATCTACACCCAcaccgg                                                                                                                           >  2:891010/1‑145 (MQ=255)
                                  aaCCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGTAGCAATTCGCAGCCATGCGAGATCTACACCAACGCTGGCAAATgc                                                                                                                    <  2:291851/150‑1 (MQ=255)
                                         aGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATg                                                                                                             <  1:1056581/150‑1 (MQ=255)
                                         aGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATg                                                                                                             <  1:491851/150‑1 (MQ=255)
                                             ccTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACTCCGTAGCGATTCGCATCCATCCGGGATCTACACCAACGCTGGCAAATGCGCGAATGCggg                                                                                                         <  2:312719/150‑1 (MQ=255)
                                              cTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCCTACACCGGCGCAAATCCCACCAAAGCCCGCTCTACACCAACGCCGGCAAAAGCGCGAAAGTGGGc                                                                                                        >  1:27686/1‑150 (MQ=255)
                                                gtgCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGACTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGCGCAATTTCCATCAAAGCCCGAACTACACCCACCCCTGCAAAAACGCGAAAGCGGGc                                                                                                        >  2:177039/1‑148 (MQ=255)
                                                 tgCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCa                                                                                                      <  1:1035812/149‑1 (MQ=255)
                                                   cagcaAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGc                                                                                                    <  1:8288/149‑1 (MQ=255)
                                                      caAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGCGCCACTCCCCTCCAATCCCGATCTACACCAAACCCCGCAAAAGCGCGCATGCGGGGCCGCACgg                                                                                                >  2:835080/1‑150 (MQ=255)
                                                       aaaCGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCGCCAATCCCATCAATCCCGGATCTCCACCAACCCCGGCAAAAACGCGAAAGCGGGGCCGCACggg                                                                                               >  2:713269/1‑150 (MQ=255)
                                                        aaCGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCCCATACACCGGCCCAATTCCCCTCAAAGCCGGGACTACACCAACACCCGCAAAAGCGCGAAAGCGGGCCACCACcgg                                                                                               >  2:817417/1‑149 (MQ=255)
                                                           gCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTaaa                                                                                           <  1:318360/150‑1 (MQ=255)
                                                            cTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAAt                                                                                          <  1:30931/150‑1 (MQ=255)
                                                            cTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAAt                                                                                          <  1:192868/150‑1 (MQ=255)
                                                                          aTAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGCGCAAATCCCCTCAATGCCGGATCTACACCAACGCCGGCAAAAGCGCGAATGCGGGCCAGCACGGGGAAATTCAAAGCCCGTGCt                                                                            >  1:10908/1‑150 (MQ=255)
                                                                            aaGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCGCCATTTTCATCAATTCCGGGTCTACACCAACACCGGCCAAATAGCGAATTCCGGGCCCCACGGGGAAAATCAAAGCCCGTGCttt                                                                          >  2:900998/1‑150 (MQ=255)
                                                                             aGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCttt                                                                          <  1:115339/149‑1 (MQ=255)
                                                                             aGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGCGCAATTCCCCTCAATACCCGGTCTTCACCCACCCCCGCCAATGCGCGAAAGCGGGCCAGCCCGGGGAAATTTCACCCCCCTGCtttt                                                                         >  2:18302/1‑149 (MQ=255)
                                                                             aGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGCCGCATACACCAGCGCCAATCCCACCAAAGCCCGATGTACACCCACACCCGCAAAAACCCGCCAGCGGGCCCACACCGGGAAATTTAACACTCGTCGTTTg                                                                         >  2:1091725/1‑150 (MQ=255)
                                                                              gATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCCTAAACCCGCGCAAATACCAACACTGCCCGATCTTCACCCACCCCCGCCAAAACGCGGAAGCGGGGCAGCACGGGGAAATTTAAATCTCCTGCttttg                                                                        >  2:466541/1‑148 (MQ=255)
                                                                                  gACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTc                                                                    <  1:401021/150‑1 (MQ=255)
                                                                                   aCTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACAACCGCGCAATTCCCCTCAAAGCCGGATCTACACCAACCCCGGCAAAAGCGCGAAAGCGGGCCCGCACCGGGAAAATTAAAGCCCGTGCTTTTGCTTCg                                                                   >  2:228562/1‑150 (MQ=255)
                                                                                         gCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACTGTAGCAATTCGCCGCCATGCCAGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCtcatc                                                             <  2:422338/150‑1 (MQ=255)
                                                                                            aaCTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCtcatcatc                                                          <  1:845018/150‑1 (MQ=255)
                                                                                            aaCTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCGCCATTCCCCTCAATGCCGGATCTACACCAACCCCGGCAAAAGCGCGAATGCGGGCCAGCACGGGGAAAATCAACGCTCGTGCTTTTGCTTCGCccatcat                                                           >  2:1050638/1‑149 (MQ=255)
                                                                                               tGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATTCACCGGCGCAATTACCCTCCAAGCCAGGTCTCCACCAACCCTGGCAAAATTGCGCAATCGGGGCCGCACGGGGAAATTTTAACCTCGCGCTTTTGCTTCTCccatccctatc                                                       >  2:432274/1‑144 (MQ=255)
                                                                                                 ccAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTAc                                                     <  1:774961/150‑1 (MQ=255)
                                                                                                     ccTACACGCTCCAGGCAACGGCGGGTCGCCTACACCCGCGCAAATCCCCACAATGCCGGGTCTACAACAAACCTGGGAAATGCGCGGATGCGGGCCAGCACGGGGAAAATCAACGCTCGTGCTTTTGGTTCCCTCCTCATCATTACCGcc                                                 >  1:393143/1‑149 (MQ=255)
                                                                                                      cTACACGCTCCAGGCAACGGCGGGTCGCCTACACCCGCGCCATTTCCCTCAATGCCCGGTCTACACCAACCCTGGCAAATGCGCGAAAGCGGGCCAGCCCGGGGAAATTCAACGCTCGTGCTTTTGCTTCGCTCATCCTCATTACCCCAg                                                >  2:162109/1‑150 (MQ=255)
                                                                                                       tACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAAt                                                                                                                      <  1:1022544/79‑1 (MQ=255)
                                                                                                           cGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTgcg                                           <  1:1032720/150‑1 (MQ=255)
                                                                                                             cTCCAGGCAACGGCGGGTCGCATACATTTTAGCGATACGGCGCACTCCGAGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGcc                                         <  2:395963/150‑1 (MQ=255)
                                                                                                                cAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATc                                      <  2:231699/150‑1 (MQ=255)
                                                                                                                  ggCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGt                                    <  1:328828/150‑1 (MQ=255)
                                                                                                                    cAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACTCCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGttt                                  <  1:945810/150‑1 (MQ=255)
                                                                                                                              tCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGatgatg                        >  1:82264/1‑150 (MQ=255)
                                                                                                                                gCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGc                       <  1:1091725/149‑1 (MQ=255)
                                                                                                                                     cacCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTAcc                 >  2:750151/1‑150 (MQ=255)
                                                                                                                                              gaTTCCCATCAATGCGAGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACCCGCTGTcac        <  2:1076375/149‑1 (MQ=255)
                                                                                                                                               aTTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACCCGCTGTcaca       <  2:27686/150‑1 (MQ=255)
                                                                                                                                                ttCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACCCGCTGTca         >  1:498174/1‑147 (MQ=255)
                                                                                                                                                 tCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACCCGCTGTCACAg      >  2:776513/1‑149 (MQ=255)
                                                                                                                                                    cATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTgcgc                                          >  2:790548/1‑110 (MQ=255)
                                                                                                                                                     aTCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGcc                                         <  1:790548/110‑1 (MQ=255)
                                                                                                                                                     aTCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACCCGCTGTCACAGAAcc  >  2:451841/1‑149 (MQ=255)
                                                                                                                                                     aTCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACCCGCTGTCACAGAAcc  >  1:87609/1‑149 (MQ=255)
                                                                                                                                                     |                                                                                                                                                    
TGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACCCGCTGTCACAGAACC  >  CP009273/2977940‑2978237

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑