Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6062,745,0800A→T 7.7% 1.9 ‑10.4 0.091216hycAregulator of the transcriptional regulator FhlA
Rejected: E-value exceeds prediction threshold.
Reads supporting (aligned to +/- strand):  new base (8/0):  ref base (19/62):  total (29/62)
Fisher's exact test strand distribution p-value = 3.14e-05
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

TTGTTTCGACGTAATACTCGATGGTGTGGCT.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGAAAATG  >  REL606/2745046‑2745115
                                   |                                   
ttGTTTCGACGTAATACTCGATGGTGTGGCT.GTTaa                                    <  1:6267972/36‑1 (MQ=255)
 tGTTTCGACGTAATACTCGATGGTGTGGCT.GTTaaa                                   <  1:3176174/36‑1 (MQ=255)
 tGTTTCGACGTAATACTCGATGGTGTGGCT.GTTaaa                                   <  1:59368/36‑1 (MQ=255)
 tGTTTCGACGTAATACTCGATGGTGTGGCT.GTTaaa                                   <  1:49650/36‑1 (MQ=255)
 tGTTTCGACGTAATACTCGATGGTGTGGCT.GTTaaa                                   <  1:3337172/36‑1 (MQ=255)
  gTTTCGACGTAATACTCGATGGTGTGGCT.GTTAAAg                                  <  1:7127209/36‑1 (MQ=255)
  gTTTCGACGTAATACTCGATGGTGTGGCT.GTTAAAg                                  <  1:1301447/36‑1 (MQ=255)
  gTTTCGACGTAATACTCGATGGTGTGGCT.GTTAAAg                                  <  1:2068458/36‑1 (MQ=255)
  gTTTCGACGTAATACTCGATGGTGTGGCT.GTTAAAg                                  <  1:1644595/36‑1 (MQ=255)
   tttCGACGTAATACTCGATGGTGTGGCT.GTTAAAGc                                 <  1:6328193/36‑1 (MQ=255)
   tttCGACGTAATACTCGATGGTGTGGCT.GTTAAAGc                                 <  1:3396306/36‑1 (MQ=255)
   tttCGACGTAATACTCGATGGTGTGGCT.GTTAAAGc                                 <  1:5651397/36‑1 (MQ=255)
    ttCGACGTAATACTCGATTGTGTGGCT.GTTAAAGcc                                <  1:2304709/36‑1 (MQ=255)
    ttCGACGTAATACTCGATGGTGTGGCT.GTTAAAGcc                                <  1:4914291/36‑1 (MQ=255)
       gACGTAATACTCGATGGTGTGGCTGGTTAAACcctt                              >  1:7526863/1‑34 (MQ=18)
       gACGTAATACTCGATGGTGTGGCT.GTTTAAAACATc                             >  1:6419505/1‑36 (MQ=21)
       gACGTAATACTCGATGGTGAGGCT.GTTAAAGCCATc                             <  1:190737/36‑1 (MQ=255)
        aCGTAATACTCGATGGTGTGGCT.GTTTAAGACaatc                            >  1:411106/1‑33 (MQ=21)
         cGTAATACTCGATGGTGTGGCT.GTTAAAGCCATCCg                           <  1:8461874/36‑1 (MQ=255)
         cGTAATACTCGATGGTGTGGCT.GTTAAAGCCATCCg                           <  1:1138507/36‑1 (MQ=255)
         cGTAATACTCGATGGTGTGGCT.GTTAAAGCCATCCg                           <  1:6442100/36‑1 (MQ=255)
          gTAATACTCGATGGTGTGGCT.GTTTAAAACATcccc                          >  1:1255317/1‑34 (MQ=18)
          gTAATACTCGATGGTGTGGCT.GTTAAAGCCATCCGc                          <  1:1791145/36‑1 (MQ=255)
          gTAATACTCGATGGTGTGGCT.GTTAAAGCCATCCGc                          <  1:3239568/36‑1 (MQ=255)
          gTAATACTCGATGGTGTGGCT.GGTTAAGCCCTcccc                          >  1:2972392/1‑34 (MQ=18)
           tAATACTCGATGGTGTGGCT.GTTGAAACCCTcctca                         >  1:468642/1‑33 (MQ=16)
           tAATACTCGATGGTGTGGCT.GTTGAAAACATACGcc                         >  1:5201446/1‑36 (MQ=16)
            aaTACTCGATGGTGTGGCT.GTTTAAAACATCCCccc                        >  1:1062858/1‑35 (MQ=16)
            aaTACTCGATGGTGTGGCT.GTTAAAGCCATCCGCCa                        <  1:1391770/36‑1 (MQ=255)
            aaTACTCGATGGTGTGGCT.GTTAAAGCCATCCGCCa                        <  1:6085015/36‑1 (MQ=255)
            aaTACTCGATGGTGTGGCT.GTTAAAGCCATCCGCCa                        <  1:6280105/36‑1 (MQ=255)
            aaTACTCGATGGTGTGGCT.GGTTAAACCCTCCCccc                        >  1:97773/1‑35 (MQ=9)
            aaTACTCGATGGTGTGGCT.GGTTAAACCATCCCccc                        >  1:1159019/1‑35 (MQ=16)
              tACTCGATGGTTTGGCT.GTTAAAGCCATCCGCCAgg                      <  1:233328/36‑1 (MQ=255)
              tACTCGATGGTGTGGGT.GTTAAAGCCATCCGCCAgg                      <  1:1542380/36‑1 (MQ=255)
              tACTCGATGGTGTGGCT.GTTAAAGCCATCCGCCAgg                      <  1:72103/36‑1 (MQ=255)
              tACTCGATGGTGTGGCT.GTTAAAGCCATCCGCCAgg                      <  1:3917115/36‑1 (MQ=255)
              tACTCGATGGTGTGGCT.GTTAAAGCCATCCGCCAgg                      <  1:1627225/36‑1 (MQ=255)
              tACTCGATGGTGTGGCT.GTTAAAGCCATCCGCCAgg                      <  1:5074211/36‑1 (MQ=255)
               aCTCGATGGTGTGGCT.GTTAAAGCCATCCGCCAggg                     <  1:3258400/36‑1 (MQ=255)
               aCTCGATGGTGTGGCT.GGTTAATACATCCGCCCggg                     >  1:6812140/1‑36 (MQ=12)
                cTCTATGTTTTGGCT.GTTAAAGCCATCCGCCAGGGt                    <  1:4751498/36‑1 (MQ=25)
                cTCGATGGTGTGGCT.GTTAAAGCCATCCGCCAGGGt                    <  1:1572531/36‑1 (MQ=255)
                cTCGATGGTGTGGCT.GTTAAAGCCATCCGCCAGGGt                    <  1:657183/36‑1 (MQ=255)
                atCGATGGTGTGGCT.GGTAAATACCTCCGCCCgggg                    >  1:7634882/2‑35 (MQ=9)
                 tCGATGGTGTGGCT.GTTAAAGCCATCCGCCAGGGTg                   <  1:7798883/36‑1 (MQ=255)
                 tCGATGGTGTGGCT.GTTAAAGCCATCCGCCAGGGTg                   <  1:1740123/36‑1 (MQ=255)
                   gATGGTGTGGCT.GTTAAAGCCATCCGCCCGGGTGAc                 <  1:4828646/36‑1 (MQ=255)
                   gATGGTGTGGCT.GTTAAAGCCATCCGCCAGGGTGAc                 <  1:908688/36‑1 (MQ=255)
                   gATGGTGTGGCT.GTTAAAGCCATCCGCCAGGGTGAc                 <  1:3478329/36‑1 (MQ=255)
                   gATGGTGTGGCT.GTTAAAGCCATCCGCCAGGGTGAc                 <  1:2726303/36‑1 (MQ=255)
                    aTGGTGTGGCT.GTTAAAGCCATCCGCCAGGGTGACg                <  1:4115029/36‑1 (MQ=255)
                     tGGTGTGGCT.GTTAAAGCCCTCCGCCAGGGTGACGt               <  1:6387299/36‑1 (MQ=255)
                     tGGTGTGGCT.GTTAAAGCCATCCGCCAGGGTGACGt               <  1:3887893/36‑1 (MQ=255)
                     tGGTGTGGCT.GTTAAAGCCATCCGCCAGGGTGACGt               <  1:3384256/36‑1 (MQ=255)
                      ggTGTGGCT.ATTAAAGCCATCCGCCAGGGTGACGTa              <  1:5395946/36‑1 (MQ=255)
                       gtgtGGCT.GTTAAAGCCATCCGCCAGGGTGACGTaa             >  1:1355354/1‑36 (MQ=255)
                       gtgtGGCT.GTTAAAGCCATCCGCCAGGGTGACGTaa             >  1:3787264/1‑36 (MQ=255)
                       gtgtGGCT.GTTAAAGCCATCCGCCAGGGTGACGTaa             <  1:3569748/36‑1 (MQ=255)
                       gtgtGGCT.GTTAAAGCCATCCGCCAGGGTGACGTaa             <  1:552460/36‑1 (MQ=255)
                        tgtgGCT.GTTAAAGCCATCCGCCAGGGTGACGTaaa            <  1:1038093/36‑1 (MQ=255)
                        tgtgGCT.GTTAAAGCCATCCGCCAGGGTGACGTaaa            <  1:6863228/36‑1 (MQ=255)
                         gtgGCT.GTTAAAGCCATCCGCCGTGGTGACTTAAAt           <  1:3043851/36‑1 (MQ=25)
                         gtgGCT.GTTAAAGCCATCCGCCAGGGTGACGTAAAt           <  1:8242288/36‑1 (MQ=255)
                         gtgGCT.GTTAAAGCCATCCGCCAGGGTGACGTAAAt           <  1:2115884/36‑1 (MQ=255)
                         gtgGCT.GTTAAAGCCATCCGCCAGGGTGACGTAAAt           <  1:3292257/36‑1 (MQ=255)
                          tgGCT.GTTAAAGCCATCCGCCAGGGTGACGTAAATg          <  1:4186330/36‑1 (MQ=255)
                          tgGCT.GTTAAAGCCATCCGCCAGGGTGACGTAAATg          >  1:8306874/1‑36 (MQ=255)
                          tgGCT.GTTAAAGCCATCCGCCAGGGTGACGTAAATg          <  1:2905005/36‑1 (MQ=255)
                           ggCT.GTTAAAGCCATCCGCCAGGGTGACGTAAATGc         >  1:3958834/1‑36 (MQ=255)
                           ggCT.GTTAAAGCCATCCGCCAGGGTGACGTAAATGc         >  1:2883324/1‑36 (MQ=255)
                           ggCT.GTTAAAGCCATCCGCCAGGGTGACGTAAATGc         >  1:5379921/1‑36 (MQ=255)
                           ggCT.GTTAAAGCCATCCGCCAGGGTGACGTAAATGc         <  1:6227766/36‑1 (MQ=255)
                            gCT.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCg        <  1:5498402/36‑1 (MQ=255)
                             cT.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGa       <  1:1537468/36‑1 (MQ=255)
                             cT.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGa       >  1:7233289/1‑36 (MQ=255)
                             cT.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGa       <  1:7220589/36‑1 (MQ=255)
                             cT.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGa       >  1:3006334/1‑36 (MQ=255)
                              t.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGaa      <  1:3014390/36‑1 (MQ=255)
                              t.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGaa      <  1:1207486/36‑1 (MQ=255)
                              t.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGaa      <  1:2333974/36‑1 (MQ=255)
                              t.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGaa      >  1:5591529/1‑36 (MQ=255)
                              t.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGaa      >  1:8060257/1‑36 (MQ=255)
                              t.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGaa      <  1:7535811/36‑1 (MQ=255)
                                gTTAAAGCCATCCGCCAGGGTGACGTAAATGCGaaa     >  1:3926121/1‑36 (MQ=255)
                                gTTAAAGCCATCCGCCAGGGTGACGTAAATGCGaaa     >  1:518143/1‑36 (MQ=255)
                                gTTAAAGCCATCCGCCAGGGTGACGTAAATGCGaaa     >  1:5794959/1‑36 (MQ=255)
                                gTTAAAGCCATCCGCCAGGGTGACGTAAATGCGaaa     <  1:6687737/36‑1 (MQ=255)
                                gTTAAAGCCATCCGCCAGGGTGACGTAAATGCGaaa     <  1:2407654/36‑1 (MQ=255)
                                 ttAAAGCCATCCGCCAGGGTGACGTAAATGCGaaaa    >  1:1647034/1‑36 (MQ=255)
                                 ttAAAGCCATCCGCCAGGGTGACGTAAATGCGaaaa    >  1:7544166/1‑36 (MQ=255)
                                 ttAAAGCCATCCGCCAGGGTGACGTAAATGCGaaaa    <  1:6343463/36‑1 (MQ=255)
                                 ttAAAGCCATCCGCCAGGGTGACGTAAATGCGaaaa    >  1:6948929/1‑36 (MQ=255)
                                 ttAAAGCCATCCGCCAGGGTGACGTAAATGCGaaaa    <  1:4184479/36‑1 (MQ=255)
                                  tAAAGCCATCCGCCAGGGTGACGTAAATGCGAAAAt   <  1:7242758/36‑1 (MQ=255)
                                  tAAAGCCATCCGCCAGGGTGACGTAAATGCGAAAAt   >  1:1556717/1‑36 (MQ=255)
                                   aaaGCCATCCGCCAGGGTGACGTAAATGCGAAAATg  <  1:3226155/36‑1 (MQ=255)
                                   aaaGCCATCCGCCAGGGTGACGGAAATGCGAAAATg  >  1:2004442/1‑36 (MQ=255)
                                   |                                   
TTGTTTCGACGTAATACTCGATGGTGTGGCT.GTTAAAGCCATCCGCCAGGGTGACGTAAATGCGAAAATG  >  REL606/2745046‑2745115

Base quality scores:  ATCG  < 3 ≤  ATCG  < 10 ≤  ATCG  < 22 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG