Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,303,984 A→C 12.1% A42A (GCT→GCG)  mdtN ← membrane fusion protein of efflux pump

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,303,9840AC12.1% 169.6 / 18.6 58A42A (GCT→GCG) mdtNmembrane fusion protein of efflux pump
Reads supporting (aligned to +/- strand):  ref base A (26/25);  new base C (4/3);  total (30/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.49e-01

CAGCTTTCGCCAGATTGGCTTCGTACGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCATGAGCGCGTCTCAAATAGATTA  >  NC_000913/4303836‑4304130
                                                                                                                                                    |                                                                                                                                                  
cAGCTTTCGCCAGATTGGCTTCGTACGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTaa                                                                                                                                                    <  4:425822/149‑1 (MQ=255)
 aGCTTTCGCCAGATTGGCTTCGTACGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAg                                                                                                                                                   <  3:438920/149‑1 (MQ=255)
    tttCGCCAGATTGGCTTCGTACGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACACTGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGt                                                                                                                                                >  1:81984/1‑149 (MQ=255)
        gCCAGATTGGCTTCGTACGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAg                                                                                                                                                   >  3:223521/1‑142 (MQ=255)
        gCCAGATTGGCTTCGTACGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAg                                                                                                                                                   <  4:223521/142‑1 (MQ=255)
         ccAGATTGGCTTCGTACGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTa                                                                                                                                           >  1:52115/1‑149 (MQ=255)
                 gCTTCGTACGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATgg                                                                                                                                   >  3:48938/1‑149 (MQ=255)
                   ttCGTACGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGgcg                                                                                                                                 <  3:471129/149‑1 (MQ=255)
                         cGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGt                                                                                                                           <  4:338166/149‑1 (MQ=255)
                                          ggAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCTTACGCGTCagca                                                                                                                                           <  4:269413/116‑4 (MQ=255)
                                          ggAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCTTACGCGTCagca                                                                                                                                           >  3:269413/1‑113 (MQ=255)
                                          ggAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACg                                                                                                          >  1:73881/1‑149 (MQ=255)
                                             aCAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGaaa                                                                                                       >  2:424301/1‑149 (MQ=255)
                                                gCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGaaaa                                                                                                      >  4:54686/1‑147 (MQ=255)
                                                gCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGaaaa                                                                                                      <  3:54686/147‑1 (MQ=255)
                                                 cAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCGGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACaa                                                                                                   <  4:48938/149‑1 (MQ=255)
                                                   aaTCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAgg                                                                                                 >  2:318057/1‑149 (MQ=255)
                                                         ccTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAAcc                                                                                           >  1:76189/1‑149 (MQ=255)
                                                         ccTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAAcc                                                                                           >  1:197689/1‑149 (MQ=255)
                                                           tGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGaa                                                                                                        >  1:53076/1‑134 (MQ=255)
                                                           tGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGaa                                                                                                        <  2:53076/134‑1 (MQ=255)
                                                                 aCTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCaaa                                                                                   <  3:206555/149‑1 (MQ=255)
                                                                  cTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAAc                                                                                  >  3:194560/1‑149 (MQ=255)
                                                                       tGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAAc                                                                             >  4:206638/1‑149 (MQ=255)
                                                                         gTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCa                                                                           >  4:341497/1‑149 (MQ=255)
                                                                                gTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAgg                                                                                                 >  2:222945/1‑120 (MQ=255)
                                                                                gTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAgg                                                                                                 <  1:222945/120‑1 (MQ=255)
                                                                                   aCCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGc                                                                 <  2:76189/149‑1 (MQ=255)
                                                                                    ccGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCa                                                                <  1:424301/149‑1 (MQ=255)
                                                                                     cGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAg                                                               >  1:401938/1‑149 (MQ=255)
                                                                                         aGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGaa                                                           <  2:81984/149‑1 (MQ=255)
                                                                                           ttCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCAc                                                                                                                              <  2:308638/80‑1 (MQ=255)
                                                                                           ttCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCAGACGCGTAAGCGTCATTAGTTGATGGCGCAc                                                                                                                              >  1:308638/1‑80 (MQ=255)
                                                                                               aCAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACt                                                     <  1:71212/149‑1 (MQ=255)
                                                                                                 aaTGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGc                                                   <  1:318057/149‑1 (MQ=255)
                                                                                                              aCTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCtttttt                                      <  2:73881/149‑1 (MQ=255)
                                                                                                                    ggTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACaga                                                                   >  1:17417/1‑114 (MQ=255)
                                                                                                                    ggTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACaga                                                                   <  2:17417/114‑1 (MQ=255)
                                                                                                                     gTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTa                               >  1:25685/1‑149 (MQ=255)
                                                                                                                          acaTCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTc                          <  2:401938/149‑1 (MQ=255)
                                                                                                                            aTCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCa                        >  3:8129/1‑149 (MQ=255)
                                                                                                                             tCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCAt                       >  1:390354/1‑149 (MQ=255)
                                                                                                                                   gTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGATTTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCATGAgcgc                 >  4:309096/1‑149 (MQ=255)
                                                                                                                                   gTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCATGAgcgc                 <  1:249172/149‑1 (MQ=255)
                                                                                                                                     aTCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCATGAGCGCGt               <  4:8129/149‑1 (MQ=255)
                                                                                                                                        taatgACGCTTACGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCATGAGCGCGtctc            >  4:21464/4‑149 (MQ=255)
                                                                                                                                         gctgACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCt                                           >  4:211313/1‑117 (MQ=255)
                                                                                                                                         gctgACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCt                                           <  3:211313/117‑1 (MQ=255)
                                                                                                                                         aatgACGCTTACGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCAt                       <  4:121031/135‑1 (MQ=255)
                                                                                                                                         aatgACGCTTACGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCAt                       >  3:121031/3‑137 (MQ=255)
                                                                                                                                          atgACGCTTACGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAgg                                                                                                 >  2:125250/2‑62 (MQ=255)
                                                                                                                                          atgACGCTTACGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAgg                                                                                                 <  1:125250/61‑1 (MQ=255)
                                                                                                                                           tgACGCGTAAGCGTCATTAGTTGATGTCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCATGAGCGCGTCTCaaa         >  3:435413/1‑149 (MQ=255)
                                                                                                                                             aCGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCATGAGCGCGTCTCAAATa       <  3:341497/149‑1 (MQ=255)
                                                                                                                                               gcgTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGc                                            >  2:303961/1‑110 (MQ=255)
                                                                                                                                               gcgTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGc                                            <  1:303961/110‑1 (MQ=255)
                                                                                                                                               gcgTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCATGAGCGCGTCTCAAATAGa     <  2:197689/149‑1 (MQ=255)
                                                                                                                                               gcgTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCATGAGCGCGTCTCAAATAGa     >  2:454088/1‑149 (MQ=255)
                                                                                                                                                  tAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCATGAGCGCGTCTCAAATAGATTa  <  2:52115/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
CAGCTTTCGCCAGATTGGCTTCGTACGGGCGCGGGTCGATGCGGAACAGCAAATCGCCCTGTTTGACTGCCTGGTTGTCGGTGACCGCCAGTTCTACAATGCGGCCGCTGACTTCCGGTACCACATCAATGGTATCTGCTGACGCGTAAGCGTCATTAGTTGATGGCGCACTGTCTACGCGCCAGATAACGAAAACAAGGGCAACCAGCGCCAACGCAACCACTAACAGAGCAGGGAATTTACTGCGAGGAGCTTTTTTCGGCGTACTTTCCATGAGCGCGTCTCAAATAGATTA  >  NC_000913/4303836‑4304130

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑