Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL606462,9140T→A 7.8% 1.2 ‑9.1 0.054intergenic (‑35/‑35)priC/ybaNprimosomal replication protein N''/conserved inner membrane protein
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (0/6):  ref base (40/8):  total (40/14)
Fisher's exact test strand distribution p-value = 1.16e-04
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

CGATAAGACCTCAATGAAAATGATAATTGTTATGCTAAAGTAGCCACTCTGTAAGCTGACAACACTCAATA  >  REL606/462879‑462949
                                   |                                   
cGATAAGACCTCAATGAAAATGATAATTGTTATGCt                                     <  1:4604752/36‑1 (MQ=255)
cGATAAGACCTCAATGAAAATGATAATTGTTATGCt                                     >  1:2286560/1‑36 (MQ=255)
cGATAAGACCTCAATGAAAATGATAATTGTTATGCt                                     >  1:2677423/1‑36 (MQ=255)
 gagaaGACCTCAATGAAAATGATAATTGTTATGCTa                                    >  1:1315646/4‑36 (MQ=255)
 gATAAGACCTCAATGAAAATGATAATTGTTATGCTa                                    >  1:163060/1‑36 (MQ=255)
 gATAAGACCTCAATGAAAATGATAATTGTTATGCTa                                    >  1:4576246/1‑36 (MQ=255)
 gATAAGACCTCAATGAAAATGATAATTGTTATGCTa                                    >  1:2427807/1‑36 (MQ=255)
 gATAAGACCTCAATGAAAATGATAATTGTTATGCTa                                    >  1:2559195/1‑36 (MQ=255)
 gATAAGACCTCAATGAAAATGATAATTGTTATGCTa                                    >  1:2758705/1‑36 (MQ=255)
  aTAAGACCTCAATGAAAATGATAATTGTTATGCTaa                                   >  1:1619471/1‑36 (MQ=255)
  aTAAGACCTCAATGAAAATGATAATTGTTATGCTaa                                   >  1:2651464/1‑36 (MQ=255)
  aTAAGACCTCAATGAAAATGATAATAGTTATGCTaa                                   >  1:4766213/1‑36 (MQ=255)
   tAAGCCCTCAATGAAAATTATAATTGTTATGCTaaa                                  <  1:817897/36‑1 (MQ=37)
    aaGACCTCAATGAAAATGATAATTGTTATGCTAAAg                                 <  1:1599109/36‑1 (MQ=255)
     aGACCTCAATGAAAATGATAATTGTTATGCTAAAGt                                <  1:4655969/36‑1 (MQ=255)
     aGACCTCAATGAAAATGATAATTGTTATGCTAAAGt                                >  1:696103/1‑36 (MQ=255)
     aGACCTCAATGAAAATGATAATTGTTATGCTAAAGt                                <  1:741415/36‑1 (MQ=255)
      gACCTCAATGAAAATGATAATTGTTATGCTAAAGTa                               <  1:3205695/36‑1 (MQ=255)
      gACCTCAATGAAAATGATAATTGTTATGCTAAAGTa                               >  1:4988404/1‑36 (MQ=255)
       aCCTCAATGAAAATGATAATTGTTATGCTAAAGTAg                              >  1:4481655/1‑36 (MQ=255)
        ccTCAATGAAAATGATAATTGTTATGCTAAAGTAGc                             <  1:186136/36‑1 (MQ=255)
        ccTCAATGAAAATGATAATTGTTATGCTAAAGTAGc                             <  1:5263611/36‑1 (MQ=255)
         cTCAATGAAAATGATAATTGTTATGCTAAAGTAGcc                            >  1:2476158/1‑36 (MQ=255)
          tCAATGAAAATGATAATTGTTATGCTAAAGTAGCCa                           >  1:2933802/1‑36 (MQ=255)
          tCAATGAAAATGATAATTGTTATGCTAAAGTAGCCa                           >  1:308432/1‑36 (MQ=255)
           cAATGAAAATGATAATTGTTATGCTAAAGTAGCCAc                          >  1:5524693/1‑36 (MQ=255)
            aaTGAAAATGATAATTGTTATGCTAAAGTAGCCAct                         >  1:1529180/1‑36 (MQ=255)
             aTGAAAATGATAATTGTTATGCTAAAGTAGCCActc                        >  1:3019963/1‑36 (MQ=255)
              tGAAAATGATAATTGTTATGCTAAAGTAGCCAatct                       >  1:3451887/1‑36 (MQ=255)
               gAAAATGATAATTGTTATGCTAAAGTAGCCACTCTg                      >  1:5796108/1‑36 (MQ=255)
               gAAAATGATAATTGTTATGCTAAAGAAGCCActctt                      >  1:3349434/1‑35 (MQ=255)
                aaaaTGATAATTGTTATGCTAAAGTAGCCACTCTGt                     >  1:3232766/1‑36 (MQ=255)
                 aaaTGATAATTGTTATGCTAAAGTAGCCACTCTGTa                    >  1:4929278/1‑36 (MQ=255)
                 aaaTGATAATTGTTATGCTAAAGTAGCCACTCTGTa                    >  1:783303/1‑36 (MQ=255)
                 aaaTGATAATTGTTATGCTAAAGTAGACACTCTGTa                    >  1:2579635/1‑36 (MQ=255)
                  aaTGATAATTGTTATGCTAAAGTAGCCACTCTGTaa                   >  1:2258762/1‑36 (MQ=255)
                  aaTGATAATTGTTATGCTAAAGTAGCCACTCTGTaa                   >  1:5898646/1‑36 (MQ=255)
                  aaTAATATTTTTAATACTAATTTAGCCACTCTGTaa                   <  1:3773579/36‑1 (MQ=0)
                   aTGATAATTGTTATGCTAAAGTAGCCACTCTGTAAg                  >  1:2919730/1‑36 (MQ=255)
                    tGATAATTGTTATGCTAAAGTAGCCACTCTGTAAGc                 >  1:4059170/1‑36 (MQ=255)
                    tGATAATTGTTATGCTAAAGGAGCCACTCTGTAAGc                 >  1:4374521/1‑36 (MQ=255)
                     gATAATTGTTATGCTAAAGTAGCAACTCTGTAAGCt                >  1:3018080/1‑36 (MQ=255)
                      aTAATTGTTATGCTAAAGTAGCCACTCTGTAAGCTg               >  1:1633753/1‑36 (MQ=255)
                       tAATTGTTATGCTAAAGTAGCCACTCTGTAAGCTGa              >  1:1967757/1‑36 (MQ=255)
                       tAATTGTTATACAAAATTAGCCACTCTGTAAGCTGa              <  1:5756836/36‑1 (MQ=25)
                        aaTTGTTATGCTAAAGTAGCCACTCTGTAAGCTGac             >  1:3760914/1‑36 (MQ=255)
                         aTTTTTATGAAAAATTAGCCACTCTGTAAGCTGaca            <  1:682709/36‑1 (MQ=16)
                           tGTTGTGCAAAAGTAGCCAATCTGTAAGCTGacaac          <  1:5705811/36‑1 (MQ=25)
                           tGTTATGCTAAAGTAGCCACTCTGTAAGCTGacaac          >  1:472639/1‑36 (MQ=255)
                           tGTTATGCAAAATTAGCCACTCTGTAAGCTGacaac          <  1:4924959/36‑1 (MQ=37)
                             ttATGCTAAAGTAGCCACTCTGTAAGCTGACAacac        >  1:940275/1‑36 (MQ=255)
                             ttATGCAAAAGTAGCCACTCTGTAAGCTGACAacac        <  1:718965/36‑1 (MQ=255)
                              tATGCTAAAGTAGCCACTCTGTAAGCTGACAACACt       >  1:5724333/1‑36 (MQ=255)
                               aTGCTAAAGTAGCCACTCTGTAAGCTGACAACACTc      >  1:264946/1‑36 (MQ=255)
                               aTGCAAAAATAGCCACTCTGTAAGCTGACAACACTc      <  1:4865813/36‑1 (MQ=37)
                                tGCTAAAGTAGCCACTCTGTAAGCTGACAACACTCa     >  1:5518324/1‑36 (MQ=255)
                                 gCTAAAGTAGCCACTCTGTAAGCTGACAACACTCaa    >  1:4216173/1‑36 (MQ=255)
                                   tAAAGTAGCCACTCTGTAAGCTGACAACACTCAata  >  1:3507984/1‑36 (MQ=255)
                                   tAAAGTAGCCACTCTGTAAGCTGACAACACTCAata  >  1:4734500/1‑36 (MQ=255)
                                   |                                   
CGATAAGACCTCAATGAAAATGATAATTGTTATGCTAAAGTAGCCACTCTGTAAGCTGACAACACTCAATA  >  REL606/462879‑462949

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 19 ≤  ATCG  < 29 ≤  ATCG  < 37 ≤  ATCG