Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913_3_pae_pgi 2,158,283 C→T 8.6% S1007S (AGC→AGT)  mdtB → multidrug efflux system, subunit B

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_pgi2,158,2830CT 8.6% 112.1 / 3.8 47S1007S (AGC→AGT) mdtBmultidrug efflux system, subunit B
Reads supporting (aligned to +/- strand):  ref base C (16/27);  new base T (2/2);  total (18/29)
Fisher's exact test for biased strand distribution p-value = 6.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.02e-01

GTCTGTTGCGTTTTCGTCCGATCCTGATGACCACTCTGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTT  >  NC_000913_3_pae_pgi/2158144‑2158431
                                                                                                                                           |                                                                                                                                                    
gTCTGTTGCGTTTTCGTCCGATCCTGATGACCACTCTGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTg                                                                                                                                             >  1:37569/1‑149 (MQ=255)
      tGCGTTTTCGTCCGACCCGGATGACCACTCTGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTg                                                                                                                                       <  2:685413/149‑1 (MQ=255)
         gTTTTCGTCCGATCCTGATGACCACTCTGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGttt                                                                                                                                    <  1:997252/149‑1 (MQ=255)
            tgcGTCCGATCCTGAGGACCACTCGGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTAcc                                                                                                                                 <  2:833190/147‑1 (MQ=255)
                tctgATCCGGATGACCCCTCGGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGc                                                                                                                             <  2:615279/146‑1 (MQ=255)
                   gATCCTGATGACCACTCTGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCAGCGCAGCACGGCGTCGTCCGTTAGGAAACGACATGTGCCTCTTGCGGATTGTCAGCCAGGTGCTGACGCGTTTTACCAcccctg                                                                                                                          >  2:714041/1‑147 (MQ=255)
                              ccACTCTGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTg                                                                                                               >  1:571737/1‑149 (MQ=255)
                               cACTCTGGCGGCTATGCTTGACGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGCTTTTTTTGc                                                                                                              >  2:83451/1‑149 (MQ=255)
                                 ctctGGCGGCTCTGCTTTGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCGGACGCTGTTTACCACGCCGGTGATTTATTTGCTg                                                                                                            <  1:145777/149‑1 (MQ=255)
                                  tctGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACTCCGGTGATTTATTTGCTGt                                                                                                           >  1:45733/1‑149 (MQ=255)
                                      gcggcTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGa                                                                                                       <  1:715368/149‑1 (MQ=255)
                                             tGCTTTGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTg                                                                                                <  1:472468/149‑1 (MQ=255)
                                                    cgcgcTGCCGCTGTTGTTGAGTACGGGGGTCGGTGGGGAACAGGGTCTGCCGTAAGTTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTTACGCTGTTTCCCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCCTtgt                                                                                         <  2:460648/149‑1 (MQ=255)
                                                     gggccgCCGCTGATGTTGCGTACTGGGGTCGGCTCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCAGGTATTGGATTGGCTGTTCGACCGCCTGGCATtgtg                                                                                        <  2:720612/144‑1 (MQ=255)
                                                       gctggggCTGATGGTGAGTACCGTGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCATGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGa                                                                                      <  1:846797/143‑1 (MQ=255)
                                                       gcTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGa                                                                                      <  1:513846/149‑1 (MQ=255)
                                                          gCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATGTTGAACCa                                                                                   >  1:290319/1‑149 (MQ=255)
                                                             tcTGATGTGGAGCACCGGTGTCGGCGCCGAACTGCGTCGTCCGTTAGGTATCGGCATGGCCGGCGGTCCGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCaaaa                                                                                <  1:775633/148‑1 (MQ=255)
                                                              gtGATGTGGAGTACGGGGGTCGGCGCGGAACTGCGTCTGCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAg                                                                               <  2:786430/148‑1 (MQ=255)
                                                              cTGATGTGGAGGACCGGGGTCGGGTCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAg                                                                               <  2:393059/149‑1 (MQ=255)
                                                                  tGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGc                                                                           <  2:37569/149‑1 (MQ=255)
                                                                    ttGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCtt                                                                         >  1:629421/1‑149 (MQ=255)
                                                                     tGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCttt                                                                        <  2:629458/149‑1 (MQ=255)
                                                                           ccGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGt                                                                  >  2:282657/1‑149 (MQ=255)
                                                                            cGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTc                                                                 >  1:309222/1‑149 (MQ=255)
                                                                             ggggTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCa                                                                <  1:173530/149‑1 (MQ=255)
                                                                                   cgcgcGGATGTGCGTCTTCCGTTTGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCCCGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAaga                                                          <  2:588374/148‑1 (MQ=255)
                                                                                    gcgcGGGACTGCGTCGTCCGTTAGGCATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTTACGCTGTTTACCACGCTGGTGATTTATTTGCTGTTCGTCCGCCTGGCATTGTGGACCATAAGCCGCTTTGCCCGTCATGAagag                                                         <  1:909351/149‑1 (MQ=255)
                                                                                     gggggAACTGCGTCGGCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGTCGCTGTTTACCACGCCGGTGATTCATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAgagg                                                        <  2:939/146‑1 (MQ=255)
                                                                                              gCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAACAGGGGGCGTAAg                                               >  2:557961/1‑149 (MQ=255)
                                                                                                gtcgtcCGTGAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTg                                             <  2:549989/149‑1 (MQ=255)
                                                                                                       gggaGGTATCGGCGTGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGACGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGtttt                                      <  2:68563/146‑1 (MQ=255)
                                                                                                         tgggTATCGGCATGGTTGGCGGTCTGATTGTCAGCGAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTGCGACCGCCTGGCAGTGTGGACCAAAAGCCGGTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGtttttt                                    <  2:99654/147‑1 (MQ=255)
                                                                                                           ggTATCGGCATGGTCGGCGGTCTGATTGTCAGTCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATtgtg                                                                                        <  1:806864/95‑1 (MQ=255)
                                                                                                           ggTATCGGCATGGTCGGCGGTCTGATTGTCAGTCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATtgtg                                                                                        >  2:806864/1‑95 (MQ=255)
                                                                                                           ggTATCGGCATGGTCGGCGGTCTGATTGTCAGTCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATtgtg                                                                                        <  1:308154/95‑1 (MQ=255)
                                                                                                           ggTATCGGCATGGTCGGCGGTCTGATTGTCAGTCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATtgtg                                                                                        >  2:308154/1‑95 (MQ=255)
                                                                                                             tATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTATTATGctc                                >  1:370401/1‑147 (MQ=255)
                                                                                                                  gCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTc                           >  1:373353/1‑149 (MQ=255)
                                                                                                                  gCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTc                           >  1:373346/1‑149 (MQ=255)
                                                                                                                                 tGATTGACAGCCAGGCACTAACGCAGTTTACCACCCCGGTGATTTATTGGCTGTTCGACCGCCTGGCATTGTAGACCAAAAGCCGCTTTGCCCGACATGAAGAGGAGGCGTAAGTGAAATTTTTTGCCCTCTTCATTTACCGCCCGATg            >  2:521444/1‑149 (MQ=255)
                                                                                                                                     tGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGcga        <  1:600007/149‑1 (MQ=255)
                                                                                                                                      ttctgCCTGGTGCTGACGTTGTTTCCCACGCCGGTGATTTATTTGCTGTTCGGCCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCGGGTGGcgac       <  2:174378/145‑1 (MQ=255)
                                                                                                                                       tCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAAGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGcgacg      >  1:51444/1‑149 (MQ=255)
                                                                                                                                        cAGCAAGGTGTTGACGCTTTTTACAACGCGGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGCCCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTAACCTCTTCATTTACCGCCCGGTGGcgacga     <  2:868698/149‑1 (MQ=255)
                                                                                                                                         aGCCGGGTGGTGGCGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGAt    <  2:835528/149‑1 (MQ=255)
                                                                                                                                         aGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGAt    >  2:398057/1‑149 (MQ=255)
                                                                                                                                           ccAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGAttt  >  1:459422/1‑149 (MQ=255)
                                                                                                                                           |                                                                                                                                                    
GTCTGTTGCGTTTTCGTCCGATCCTGATGACCACTCTGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTT  >  NC_000913_3_pae_pgi/2158144‑2158431

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑