Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6062,241,5870A→G 7.5% 1.4 ‑5.3 ‑0.067813ccmHheme lyase, CcmH subunit
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (5/0):  ref base (19/41):  total (25/42)
Fisher's exact test strand distribution p-value = 5.15e-03
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 9.90e-01

CGCAGCAGTTCACCACCGAGGCGGTTGTCGTTGGGATCAGATGAACGTGTCAACGCTTCAGCATAACCCAG  >  REL606/2241552‑2241622
                                   |                                   
cgcAGCAGTTCACCACCGAGGCGGTTGTCGTTGGGa                                     <  1:2811954/36‑1 (MQ=255)
 gcggcagTGCACCGCCGAGGCGGTTGTCGTTGGGAt                                    <  1:5533321/33‑1 (MQ=25)
 gcagcaTTACACCACCGAGGCGGTTGTCGTTGGGAt                                    <  1:5719223/36‑1 (MQ=37)
 gcagcaGTTCACCACCGAGGCGGTTGTCGTTGGGAt                                    <  1:6869400/36‑1 (MQ=255)
   agcagTTCACCACCGAGGCGGTTGTCGTTGGGATCa                                  <  1:6987642/36‑1 (MQ=255)
    gcagTTCACCACCGAGGCGGTTGTCGTTGGGATCAg                                 <  1:1176554/36‑1 (MQ=255)
    gcaaTTCACCACCGAGGCGGTTGTCGTTGGGATCAg                                 <  1:1649442/36‑1 (MQ=255)
      agTTCACCACCGAGGCGGTTGTCGTTGGGATCAGAt                               <  1:7016958/36‑1 (MQ=255)
      agTTCACCACCGAGGCGGTTGTCGTTGGGATCAGAt                               <  1:1672622/36‑1 (MQ=255)
       gTTCACCACCGAGGCGGTTGTCGTTGGGATCAGATg                              <  1:6841811/36‑1 (MQ=255)
       gTTCACCACCGAGGCGGTTGTCGTTGGGATCAGATg                              <  1:3936229/36‑1 (MQ=255)
        ttCACCACCGAGGCGGTTGTCGTTGGGATCAGATGa                             <  1:3437209/36‑1 (MQ=255)
         tCACCACCGAGGCGGTTTTCGTTGGGGTCAGATGaa                            >  1:4613632/1‑36 (MQ=37)
          caccgcCGATGCGGTTGTCGTTGGGATCAGATGAAc                           <  1:6231707/36‑1 (MQ=37)
          caccacCGAGGCGGTTGTCGTTGGGATCAGATGAAc                           <  1:3177373/36‑1 (MQ=255)
          caccacCGAGGCGGGTGTCGTTGTGGTTTGATGaaa                           >  1:3838944/1‑35 (MQ=12)
           accaccGAGGCGGTTTTTGTTTTGGTTAGATGaaag                          >  1:4125682/1‑34 (MQ=2)
           accaccGAGGCGGTTGTCGTTGGGGTCAGATGAACg                          >  1:1350653/1‑36 (MQ=255)
           accaccGAGGCGGTTGTCGTTGGGATCAGATGAACg                          <  1:4940617/36‑1 (MQ=255)
            ccgccGAGGCGGTTGTCGTTGGGATCAGATGAACgt                         <  1:7804692/33‑1 (MQ=255)
            ccaccGAGGCGGTTGTCGTTGGGATCAGATGAAcat                         <  1:159421/36‑3 (MQ=255)
            ccaccGAGGCGGTTGTCGTTGGGATCAGATGAACgt                         <  1:5112766/36‑1 (MQ=255)
             caccGAGGCGGTCGTCGGTGGGCTCACATGAACgtg                        >  1:2666947/1‑36 (MQ=16)
              accGAGGCGGTTTTCTTTTGGGTCAGATGGAAgtgt                       >  1:6856596/1‑36 (MQ=9)
              accGAGGCGGTTGTCGTTGGGATCAGATGAACgtgt                       <  1:469226/36‑1 (MQ=255)
                cGAGGCGGTTGTCGTTGGGATCAGATGAACGTGTCa                     <  1:350925/36‑1 (MQ=255)
                cGAGGCGGTTGTCGTTGGGATCAGATGAACGTGTCa                     <  1:3516369/36‑1 (MQ=255)
                  gggCGGTTGTCGTTGGGATAAGATGAACGTGTCAAc                   <  1:5737369/35‑1 (MQ=38)
                  aGGCGGTTGTCGTTGGGCTCAGATGAACGTGTCAAc                   <  1:7250756/36‑1 (MQ=255)
                  aGGCGGTTGTCGTTGGGATCAGATGAACGTGTCAAc                   <  1:6718565/36‑1 (MQ=255)
                  aGGCGGTTGTCGTTGGGATCAGATGAACGTGTCAAc                   <  1:3186421/36‑1 (MQ=255)
                  aGGCGGTTGTCGTTGGGATCAGATGAACGTGTCAAc                   <  1:1527030/36‑1 (MQ=255)
                   tgCGCTTGTTGTCGGGATCAGATGCACGTGTCAAct                  <  1:3137835/35‑2 (MQ=16)
                    gCGGTTGTCGTTGGGATCAGATGAACGTGTCAACGc                 <  1:5734222/36‑1 (MQ=255)
                    gCGGTTGTCGTTGGGATCAGATGAACGTGTCAACGc                 <  1:3824418/36‑1 (MQ=255)
                     cGGTTGTCGTTGGGATCAGATGAACGTGTCAACGCt                <  1:3873663/36‑1 (MQ=255)
                     cGGTTGTCGTTGGGATCAGATGAACGTGTCAACGCt                <  1:456707/36‑1 (MQ=255)
                      ggTTGTCGTTGGGATCAGATGAACGTGTCAACGCtt               >  1:1448292/1‑36 (MQ=255)
                       gTTGTCGTTGGGATCAGATGAACGTGTCAACGCttt              <  1:1240998/36‑2 (MQ=255)
                       gTTGTCGTTGGGATCAGATGAACGTGTCAACGCTTc              >  1:5321818/1‑36 (MQ=255)
                       gTTGTCGTTGGGATCAGATGAACGTGTCAACGCTTc              <  1:3984454/36‑1 (MQ=255)
                       gTTGTCGTTGGGATCAGATGAACGTGTCAACGCTTc              >  1:2163666/1‑36 (MQ=255)
                       gTTGTCGTTGGGATCAGATGAACGTGTCAACGCTTc              <  1:2940501/36‑1 (MQ=255)
                         tGTCGTTGGGATCAGATGAACGTGTCAACGCTTCAg            >  1:1108550/1‑36 (MQ=255)
                          gTCGTTGGGATCAGATGAACGTGTCAACGCTTCAGc           <  1:4299247/36‑1 (MQ=255)
                          gTCGTTGGGATCAGATGAACGTGTCAACGCTTCAGc           <  1:6315124/36‑1 (MQ=255)
                           tCGTTGGGATCAGATGAACGTGTCAACGCTTCAGCa          <  1:6908008/36‑1 (MQ=255)
                           tCGTTGGGATCAGATGAACGTGTCAACGCTTCAGCa          >  1:6431767/1‑36 (MQ=255)
                            cGTTGGGATCAGATGAACGTGTCAACGCTTCAGCAt         >  1:6266333/1‑36 (MQ=255)
                            cGTTGGGATCAGATGAACGTGTCAACGCTTCAGCAt         >  1:1813938/1‑36 (MQ=255)
                            cGTTGGGATCAGATGAACGTGTCAACGCTTCAGCAt         >  1:3613513/1‑36 (MQ=255)
                            cGTTGGGATCAGATGAACGTGTCAACGCTTCAGCAt         <  1:3079641/36‑1 (MQ=255)
                             gTTGGGATCAGATGAACGTGTCAACGCTTCAGCATa        <  1:7457212/36‑1 (MQ=255)
                             gTTGGGATCAGATGAACGTGTCAACGCTTCAGCATa        >  1:6047131/1‑36 (MQ=255)
                             gTTGGGATCAGATGAACGTGGCAACGCTTCAGCATa        >  1:4146189/1‑36 (MQ=255)
                              ttGGGATCAGATGAACGTGTCAACGCTTCAGTATaa       >  1:2807529/1‑36 (MQ=255)
                              ttGGGATCAGATGAACGTGTCAACGCTTCAGCATaa       <  1:2581293/36‑1 (MQ=255)
                              ttGGGATCAGATGAACGTGTCAACGCTTCAGCATaa       <  1:7248942/36‑1 (MQ=255)
                              ttGGGATCAGATGAACGTGTCAACGCTTCAGCATaa       >  1:1179126/1‑36 (MQ=255)
                              ttGGGATCAGATGAACGTGTCAACGCTTCAGCATaa       >  1:1243995/1‑36 (MQ=255)
                              ttGGGATCAGATGAACGTGTCAACGCTTCAGCATaa       >  1:6578464/1‑36 (MQ=255)
                              ttGGGATCAGATGAACGTGTCAACGCTTCAGCATaa       >  1:6268168/1‑36 (MQ=255)
                               tGGGATCAGATGAACGTGTCAACGCTTCAGCATAAc      >  1:577980/1‑36 (MQ=255)
                                gggATCAGATGAACGTGTCAACGCTTCAGCATAAcc     <  1:5559306/36‑1 (MQ=255)
                                 ggATCAGATGAACGTGTCAACGCTTCAGCATAAccc    <  1:3420085/36‑1 (MQ=255)
                                 ggATCAGATGAACGTGTCAACGCTTCAGCATAAccc    >  1:7511931/1‑36 (MQ=255)
                                  gATCAGATGAACGTGTGAACGCTTCAGCATAACCCa   >  1:2394919/1‑36 (MQ=255)
                                  gATCAGATGAACGTGTCAACCCTTCAGCATAACACa   >  1:6732032/1‑36 (MQ=38)
                                   aTCAGATGAACGTGTCAACGCTTCAGCATAACCCAg  <  1:1266216/36‑1 (MQ=255)
                                   aTCAGATGAACGTGTCAACGCTTCAGCATAACCCAg  >  1:5547968/1‑36 (MQ=255)
                                   aTCAGATGAACGTGTCAACGCTTCAGCATAACCCAg  >  1:2463286/1‑36 (MQ=255)
                                   aTCAGATGAACGTGTCAACGCTTCAGCATAACCCAg  >  1:6043525/1‑36 (MQ=255)
                                   aTCAGATGAACGTGTCAACGCTTCAGCATAACCCAg  <  1:1344476/36‑1 (MQ=255)
                                   |                                   
CGCAGCAGTTCACCACCGAGGCGGTTGTCGTTGGGATCAGATGAACGTGTCAACGCTTCAGCATAACCCAG  >  REL606/2241552‑2241622

Base quality scores:  ATCG  < 3 ≤  ATCG  < 9 ≤  ATCG  < 20 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG