Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,000,2400C→G19.1% 11.047A226G (GCT→GGT) fluantigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  new base (9/0):  ref base (12/26):  total (21/26)

CACCATCAATGAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACAGCAAATACCACTGTGGTTTATGCCG  >  REL606/3000205‑3000275
                                   |                                   
caccaTGTATGAAAATGGTCGTCAGATTGTGgctgc                                     <  1:7327529/36‑1 (MQ=21)
caccaTCAATGAAAATGGTCGCCAGATTGTGgctgc                                     >  1:3456045/1‑36 (MQ=255)
  ccaTCAATGAAAATGGTCGTCAGATTGTGGctggtg                                   >  1:6653225/1‑36 (MQ=255)
  ccaTCAATGAAAATGGTCGTCAGATTGTGGctgctg                                   <  1:5337246/36‑1 (MQ=255)
  ccaTCAATGAAAATGGTCGTCAGATTGTGGctgctg                                   <  1:5591724/36‑1 (MQ=255)
   caTCAATGAAGATGGTCGTCAGATTGTGGCTGCTGa                                  <  1:1198610/36‑1 (MQ=255)
    aTCAATGAAAATGGTCGTCAGATTGTGGCTGCTGaa                                 <  1:5643560/36‑1 (MQ=255)
    aTCAATGAAAATGGTCGCCAGACTGACGCCGCTGaa                                 >  1:1210645/1‑36 (MQ=12)
     tCAATGAAAATGGTCGTCAGATTGTGGCTGCTGAAg                                <  1:7343400/36‑1 (MQ=255)
      cAATGAAAATGGTCGTCAGATTGTGGCTGGTGTAgg                               >  1:5171656/1‑36 (MQ=21)
      cAATGAAAATGGTCGTCAGATTGTGGCTGGTGGAgg                               >  1:6323321/1‑36 (MQ=21)
       aaTGAAAATGGTTGTCAGATTGTGGCTGCTGAAGGa                              <  1:3061665/36‑1 (MQ=255)
       aaTGAAAATGGTCGTCAGATTGTGGCTGGTGGAGGa                              >  1:5564082/1‑36 (MQ=21)
        aTGAATATGGTCGTCAGATTGTGGCTGGTGGAGGaa                             >  1:1937671/1‑36 (MQ=21)
        aTGAAAATGGTCGTCAGATTGTGGCTGGTGGAAGaa                             >  1:2633530/1‑36 (MQ=18)
        aTGAAAATGGTCGTCAGATTGTGGCTGCTGAAGGaa                             <  1:5327823/36‑1 (MQ=255)
         taaaaaTGGTCGTCAGATTGTGGCTGCTGAAGGAAc                            <  1:1659124/34‑1 (MQ=255)
         tGAGAAGGGTCGTCAGATTGTGGCTGCTGAAGGAAc                            <  1:5338435/36‑1 (MQ=25)
         tGAAAATGGTCGTCAGATTGTGGCTGGTGGAgggaa                            >  1:5826125/1‑33 (MQ=18)
         tGAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAAc                            <  1:644312/36‑1 (MQ=255)
          gAAAATGGTCGTCAGATTGTGGCTGGTGACAGAACa                           >  1:6149545/1‑36 (MQ=18)
          gAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACa                           <  1:2954025/36‑1 (MQ=255)
          gAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACa                           <  1:4666973/36‑1 (MQ=255)
          gAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACa                           <  1:6680660/36‑1 (MQ=255)
          gAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACa                           <  1:1475971/36‑1 (MQ=255)
          gAAAAGGGGCGGGAGATTGTGGCTGCTGAAGGAACa                           <  1:3198621/36‑1 (MQ=18)
            aaaTGGTCGTCAGATTGTGGCTGCTGAAGGAACAGc                         <  1:117022/36‑1 (MQ=255)
            aaaTGGTCGTCAGATTGTGGCTGCTGAAGGAACAGc                         <  1:1835942/36‑1 (MQ=255)
             aaTGGTCGTCAGATTGTGGCTGCTGAAGGAACAGCa                        <  1:6506864/36‑1 (MQ=255)
             aaTGGTCGTCAGATTGTGGCTGCGGAAACAACAACa                        >  1:2419487/1‑36 (MQ=18)
              aTGGTCGTCAGATTGTGGCTGCTGAAGGAACAGCaa                       <  1:2386151/36‑1 (MQ=255)
              aTGGTCGTCAGATTGTGGCTGCTGAAGGAACAGCaa                       <  1:6040618/36‑1 (MQ=255)
               tGGTCGTCAGATTGTGGCTGCTGGAGGGACAGGaaa                      >  1:5263820/1‑36 (MQ=21)
                ggTCGTCAGATTGTGGCTGGTGAAGGAAAAGAaaaa                     >  1:667823/1‑35 (MQ=18)
                 gtcgtcAGATTGTGGCTGCTGAAGGAACAGCAAATa                    <  1:1779263/36‑1 (MQ=255)
                 gtcgtcAGATTGTGGCTGCTCTAGGAAAAACaaaaa                    >  1:6632696/1‑34 (MQ=18)
                 gtcatcAGATTGTGGCTGCTGAAGGAACAGCAAATa                    <  1:4256368/36‑1 (MQ=255)
                   cgtcAGATTGTGGCTGGCGAAGGAAAAGGCAATaaa                  >  1:391100/1‑34 (MQ=9)
                   cgtcAGATTGTGGCTGCTGAAGGAACAGCAAATAcc                  >  1:4657346/1‑36 (MQ=255)
                    gtcAGATTGTGGCTGCTGAAGGAACAGCAAATACCa                 <  1:5849020/36‑1 (MQ=255)
                    gtcAGATTGTGGCTGCTGAAGGAACAGCAAATACCa                 <  1:6331449/36‑1 (MQ=255)
                      cAGATTGTGGCTGCTGGAGGGAAAGCAAATCCCCCt               >  1:4761309/1‑36 (MQ=12)
                      cAGATTGTGGCTGCTGAAGGAACAGCAAATACCACt               <  1:2206632/36‑1 (MQ=255)
                       aGATTGTGGCTGCTGAAGGAACACCCAAACCCACtg              >  1:791014/1‑36 (MQ=18)
                       aGATTGTGGCTGCTGAAGGAAAAGCAAAAACCCCtt              >  1:6804248/1‑35 (MQ=18)
                             tgGCTGCTGAAGGAACAGCAAATACCACTGTGGttt        >  1:5272237/1‑36 (MQ=255)
                             tgGCTGCTGAAGGAACAGCAAATACCACTGTGGttt        <  1:6724806/36‑1 (MQ=255)
                             tgGCTGCTGAAGGAACAGCAAATACCACTCTGGttt        >  1:5767544/1‑36 (MQ=255)
                             tgGCTCCTGAAGGAACAGCAAATACCACTGTGGttt        <  1:6551945/36‑1 (MQ=255)
                              ggCTGCTGAAGGAACAGCAAATACCACTGTGGTTTa       >  1:5924434/1‑36 (MQ=255)
                              ggCTGCTGAAGGAACAGCAAATACCACTGTGGTTTa       >  1:2676416/1‑36 (MQ=255)
                              ggCTGCAAAAGGAACAGCAAATACCACTGTGGTTTa       <  1:4949830/36‑1 (MQ=25)
                               gctgctGAAGGAACAGCAAATACCACTGTGGTTTAt      <  1:1650119/36‑1 (MQ=255)
                               gctgctGAAGGAACAGCAAATACCACTGTGGTTTAt      <  1:4970721/36‑1 (MQ=255)
                                ctgctgAAGGAACAGCAAATACCACTGTGGATCATg     >  1:5189746/1‑36 (MQ=25)
                                 tgctgAAGGAACAGCAAATACCACTGTGGTTTGTGc    >  1:6010634/1‑36 (MQ=255)
                                 tgctgAAGGAACAGCAAATACCACTGTGGTTTATGc    <  1:7069590/36‑1 (MQ=255)
                                 tgctgAAGGAACAGCAAATACCACTGTGGTTTATGc    >  1:1283335/1‑36 (MQ=255)
                                   ctgAAGGAACAGCAAATACCACTGTGGTTTATGCcg  <  1:5382786/36‑1 (MQ=255)
                                   ctgAAGGAACAGCAAATACCACTGTGGTTTATGCcg  >  1:7400436/1‑36 (MQ=255)
                                   |                                   
CACCATCAATGAAAATGGTCGTCAGATTGTGGCTGCTGAAGGAACAGCAAATACCACTGTGGTTTATGCCG  >  REL606/3000205‑3000275

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