Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,000,2400C→G20.8% 12.048677fluantigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  new base (10/0):  ref base (12/26):  total (22/26)

CACCATCAATGAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACAGCAAATACCACTGTGGTTTATGCCG  >  REL606/3000205‑3000275
                                   |                                   
caccaTGTATGAAAATGGTCGTCAGATTGTGgctgc                                     <  2:3588319/36‑1 (MQ=37)
caccaTCAATGAAAATGGTCGCCAGATTGTGgctgc                                     >  1:3456045/1‑36 (MQ=255)
  ccaTCAATGAAAATGGTCGTCAGATTGTGGctggtg                                   >  2:2914015/1‑36 (MQ=255)
  ccaTCAATGAAAATGGTCGTCAGATTGTGGctgctg                                   <  2:1852514/36‑1 (MQ=255)
  ccaTCAATGAAAATGGTCGTCAGATTGTGGctgctg                                   <  2:1598036/36‑1 (MQ=255)
   caTCAATGAAGATGGTCGTCAGATTGTGGCTGCTGa                                  <  1:1198610/36‑1 (MQ=255)
    aTCAATGAAAATGGTCGTCAGATTGTGGCTGCTGaa                                 <  2:1904350/36‑1 (MQ=255)
    aTCAATGAAAATGGTCGCCAGACTGACGCCGCTGaa                                 >  1:1210645/1‑36 (MQ=12)
     tCAATGAAAATGGTCGTCAGATTGTGGCTGCTGAAg                                <  2:3604190/36‑1 (MQ=255)
      cAATGAAAATGGTCGTCAGATTGTGGCTGGTGTAgg                               >  2:1432446/1‑36 (MQ=37)
      cAATGAAAATGGTCGTCAGATTGTGGCTGGTGGAgg                               >  2:2584111/1‑36 (MQ=37)
       aaTGAAAATGGTTGTCAGATTGTGGCTGCTGAAGGa                              <  1:3061665/36‑1 (MQ=255)
       aaTGAAAATGGTCGTCAGATTGTGGCTGGTGGAGGa                              >  2:1824872/1‑36 (MQ=37)
        aTGAATATGGTCGTCAGATTGTGGCTGGTGGAGGaa                             >  1:1937671/1‑36 (MQ=25)
        aTGAAAATGGTCGTCAGATTGTGGCTGGTGGAAGaa                             >  1:2633530/1‑36 (MQ=21)
        aTGAAAATGGTCGTCAGATTGTGGCTGCTGAAGGaa                             <  2:1588613/36‑1 (MQ=255)
         taaaaaTGGTCGTCAGATTGTGGCTGCTGAAGGAAc                            <  1:1659124/34‑1 (MQ=255)
         tGAGAAGGGTCGTCAGATTGTGGCTGCTGAAGGAAc                            <  2:1599225/36‑1 (MQ=37)
         tGAAAATGGTCGTCAGATTGTGGCTGGTGGAgggaa                            >  2:2086915/1‑33 (MQ=21)
         tGAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAAc                            <  1:644312/36‑1 (MQ=255)
          gAAAATGGTCGTCAGATTGTGGCTGGTGACAGAACa                           >  2:2410335/1‑36 (MQ=21)
          gAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACa                           <  2:2941450/36‑1 (MQ=255)
          gAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACa                           <  2:927763/36‑1 (MQ=255)
          gAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACa                           <  1:1475971/36‑1 (MQ=255)
          gAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACa                           <  1:2954025/36‑1 (MQ=255)
          gAAAAGGGGCGGGAGATTGTGGCTGCTGAAGGAACa                           <  1:3198621/36‑1 (MQ=16)
            aaaTGGTCGTCAGATTGTGGCTGCTGAAGGAACAGc                         <  1:117022/36‑1 (MQ=255)
            aaaTGGTCGTCAGATTGTGGCTGCTGAAGGAACAGc                         <  1:1835942/36‑1 (MQ=255)
             aaTGGTCGTCAGATTGTGGCTGCTGAAGGAACAGCa                        <  2:2767654/36‑1 (MQ=255)
             aaTGGTCGTCAGATTGTGGCTGCGGAAACAACAACa                        >  1:2419487/1‑36 (MQ=16)
              aTGGTCGTCAGATTGTGGCTGCTGAAGGAACAGCaa                       <  2:2301408/36‑1 (MQ=255)
              aTGGTCGTCAGATTGTGGCTGCTGAAGGAACAGCaa                       <  1:2386151/36‑1 (MQ=255)
               tGGTCGTCAGATTGTGGCTGCTGGAGGGACAGGaaa                      >  2:1524610/1‑36 (MQ=25)
                ggTCGTCAGATTGTGGCTGGTGAAGGAAAAGAaaaa                     >  1:667823/1‑35 (MQ=21)
                 gtcgtcAGATTGTGGCTGCTGAAGGAACAGCAAATa                    <  1:1779263/36‑1 (MQ=255)
                 gtcgtcAGATTGTGGCTGCTCTAGGAAAAACaaaaa                    >  2:2893486/1‑34 (MQ=16)
                 gtcatcAGATTGTGGCTGCTGAAGGAACAGCAAATa                    <  2:517158/36‑1 (MQ=255)
                   cgtcAGATTGTGGCTGGCGAAGGAAAAGGCAATaaa                  >  1:391100/1‑34 (MQ=9)
                   cgtcAGATTGTGGCTGCTGAAGGAACAGCAAATAcc                  >  2:918136/1‑36 (MQ=255)
                    gtcAGATTGTGGCTGCTGAAGGAACAGCAAATACCa                 <  2:2109810/36‑1 (MQ=255)
                    gtcAGATTGTGGCTGCTGAAGGAACAGCAAATACCa                 <  2:2592239/36‑1 (MQ=255)
                      cAGATTGTGGCTGCTGGAGGGAAAGCAAATCCCCCt               >  2:1022099/1‑36 (MQ=12)
                      cAGATTGTGGCTGCTGAAGGAACAGCAAATACCACt               <  1:2206632/36‑1 (MQ=255)
                       aGATTGTGGCTGCTGAAGGAACACCCAAACCCACtg              >  1:791014/1‑36 (MQ=16)
                       aGATTGTGGCTGCTGAAGGAAAAGCAAAAACCCCtt              >  2:3065038/1‑35 (MQ=18)
                        gATTGTGGCTGGTGGAGGAAAAGCCAATACCACtgg             >  2:3413659/1‑35 (MQ=16)
                             tgGCTGCTGAAGGAACAGCAAATACCACTGTGGttt        >  2:1533027/1‑36 (MQ=255)
                             tgGCTGCTGAAGGAACAGCAAATACCACTGTGGttt        <  2:2985596/36‑1 (MQ=255)
                             tgGCTGCTGAAGGAACAGCAAATACCACTCTGGttt        >  2:2028334/1‑36 (MQ=255)
                             tgGCTCCTGAAGGAACAGCAAATACCACTGTGGttt        <  2:2812735/36‑1 (MQ=255)
                              ggCTGCTGAAGGAACAGCAAATACCACTGTGGTTTa       >  1:2676416/1‑36 (MQ=255)
                              ggCTGCTGAAGGAACAGCAAATACCACTGTGGTTTa       >  2:2185224/1‑36 (MQ=255)
                              ggCTGCAAAAGGAACAGCAAATACCACTGTGGTTTa       <  2:1210620/36‑1 (MQ=37)
                               gctgctGAAGGAACAGCAAATACCACTGTGGTTTAt      <  2:1231511/36‑1 (MQ=255)
                               gctgctGAAGGAACAGCAAATACCACTGTGGTTTAt      <  1:1650119/36‑1 (MQ=255)
                                ctgctgAAGGAACAGCAAATACCACTGTGGATCATg     >  2:1450536/1‑36 (MQ=37)
                                 tgctgAAGGAACAGCAAATACCACTGTGGTTTGTGc    >  2:2271424/1‑36 (MQ=255)
                                 tgctgAAGGAACAGCAAATACCACTGTGGTTTATGc    <  2:3330380/36‑1 (MQ=255)
                                 tgctgAAGGAACAGCAAATACCACTGTGGTTTATGc    >  1:1283335/1‑36 (MQ=255)
                                   ctgAAGGAACAGCAAATACCACTGTGGTTTATGCcg  >  2:3661226/1‑36 (MQ=255)
                                   ctgAAGGAACAGCAAATACCACTGTGGTTTATGCcg  <  2:1643576/36‑1 (MQ=255)
                                   |                                   
CACCATCAATGAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACAGCAAATACCACTGTGGTTTATGCCG  >  REL606/3000205‑3000275

Base quality scores:  ATCG  < 3 ≤  ATCG  < 6 ≤  ATCG  < 13 ≤  ATCG  < 27 ≤  ATCG  < 32 ≤  ATCG