Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,976,793 C→A 8.6% H153N (CAC→AAC)  PP_1770 → 3‑phosphoshikimate 1‑carboxyvinyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,976,7930CA 8.6% 139.3 / 4.1 47H153N (CAC→AAC) PP_17703‑phosphoshikimate 1‑carboxyvinyltransferase
Reads supporting (aligned to +/- strand):  ref base C (17/25);  new base A (2/2);  total (20/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.16e-01

CCGACGTCGGCAGCGCCAAGGGCAACGTCGTGCGTGAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGAAGTACTGGCCGCCACCAGCCATCTGC  >  NC_002947/1976647‑1976937
                                                                                                                                                  |                                                                                                                                                 
ccGACGTCGGCAGCGCCAAGGGCAACGTCGTGCGTGAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGcac                                                                                                                                                 <  4:142955/149‑1 (MQ=255)
   aCGTCGGCAGCGCCAAGGGCAACGTCGTGCGTGAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAg                                                                                                                                              <  1:253366/149‑1 (MQ=255)
   aCGTCGGCAGCGCCAAGGGCAACGTCGTGCGTGAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAg                                                                                                                                              <  8:95534/149‑1 (MQ=255)
   aCGGCGGCAGCGCCACGGGCAACGTCGGGCGTGAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGGTTCGTCCCGGGCCACCCCATCGCCGGTTCCGGGCAGAGCGGGGTAGAGGCGTCCAATGGCACCTTGTTCCGCCGGCACAAg                                                                                                                                              <  4:252441/149‑1 (MQ=255)
      tCGGCAGCGCCAAGGGCAACGTCGTGCGTGAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTc                                                                                                                                           <  7:84775/149‑1 (MQ=255)
      tCGGCAGCGCCAAGGGCAACGTCGTGCGGGAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTGCCGGCGGAACAAGGtg                                                                                                                                           <  3:271607/149‑2 (MQ=255)
         gCAGCGCCAAGGGCAACGTCGTGCGTGAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATc                                                                                                                                        <  4:77391/149‑1 (MQ=255)
           aGCGCCAAGGGCAACGTCGTGCGTGAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCt                                                                                                                                      <  5:184925/149‑1 (MQ=255)
                       aaCGTCGTGCGTGAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGc                                                                                                                          >  5:124304/1‑149 (MQ=255)
                             gtgcgtgAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAAc                                                                                                                    <  6:292317/149‑1 (MQ=255)
                               gcgtgAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCCTCGCCGGTTCCGAGCAGAGCGGGGTAAAGGCGTCCAATGCCACCATGTTCCGCCGGGACAAGGTCATCCACCCCCCGCTGGCCGAAACCg                                                                                                                  >  4:151193/1‑149 (MQ=255)
                               gcgtgAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCAcg                                                                                                                                  <  6:108871/133‑1 (MQ=255)
                               gcgtgAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCAcg                                                                                                                                  >  5:108871/1‑133 (MQ=255)
                                              cGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGca                                                                                                                                                  >  7:196807/1‑102 (MQ=255)
                                              cGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGca                                                                                                                                                  <  8:196807/102‑1 (MQ=255)
                                              cGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTgg                                                                                                   <  1:254122/149‑1 (MQ=255)
                                               gTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGt                                                                                                  >  4:161759/1‑149 (MQ=255)
                                                     ggTGCCCGCCTGGCGCGCTTCGTCCCGGTCCACCGCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCTCCGGCACAAGGTCATCCTCACGCCGCTTGCCGAAACCGACCCCCGCGCGCTGGTCCTgg                                                                                             <  8:162752/148‑1 (MQ=255)
                                                     ggTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGt                                                                                            >  8:276233/1‑149 (MQ=255)
                                                         cccGCCTGCCGCGCTTCGTCCCGGGCCACACCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCATGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGAc                                                                                        >  5:278229/1‑149 (MQ=255)
                                                          ccGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGAcc                                                                                       >  2:286203/1‑149 (MQ=255)
                                                                 ccGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCtg                                                                                  <  3:161759/147‑1 (MQ=255)
                                                                           tCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTg                                                                     >  6:221441/1‑149 (MQ=255)
                                                                               gggCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTgc                                                                         <  5:192132/141‑1 (MQ=255)
                                                                               gggCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTgc                                                                         >  6:192132/1‑141 (MQ=255)
                                                                                   cACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGa                                                             <  6:124304/149‑1 (MQ=255)
                                                                                     ccccATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGAtg                                                           >  6:368276/1‑149 (MQ=255)
                                                                                                   ccGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCTGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGAtgtg                                                         <  2:337377/137‑1 (MQ=255)
                                                                                                   ccGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGAtgtg                                                         >  1:337377/1‑137 (MQ=255)
                                                                                                          gagCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAgc                                      <  1:188218/149‑1 (MQ=255)
                                                                                                          gagCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGGTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAgc                                      <  5:221441/149‑1 (MQ=255)
                                                                                                          gagCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCACGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAgc                                      >  5:185600/1‑149 (MQ=255)
                                                                                                             cGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTGCTGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAgcgc                                    <  1:256694/149‑1 (MQ=255)
                                                                                                                  tAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCACGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGAc                              <  6:185600/149‑1 (MQ=255)
                                                                                                                  gcgagGCGTCCAATGCCTCCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCTTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGAc                              <  6:232109/147‑1 (MQ=255)
                                                                                                                         gTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCAGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGAAGTAc                       >  8:39774/1‑149 (MQ=255)
                                                                                                                            cAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGAAGTACTgg                    >  5:370691/1‑149 (MQ=255)
                                                                                                                            cAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGAAGTACTgg                    <  7:109472/149‑1 (MQ=255)
                                                                                                                              aTGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGAAGTACTGgcc                  <  5:368276/149‑1 (MQ=255)
                                                                                                                                gCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGAAGTACTGgccgc                >  4:118799/1‑149 (MQ=255)
                                                                                                                                atgaCCTTGTGCCGGCGGAACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGaa                           <  7:192878/135‑1 (MQ=255)
                                                                                                                                atgaCCTTGTGCCGGCGGAACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGaa                           >  8:192878/4‑138 (MQ=255)
                                                                                                                                  gaCCTTGTGCCGGCGGAACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGAAGTACTGGCAGcca              >  8:328793/2‑149 (MQ=255)
                                                                                                                                   aCCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGcc                                   <  7:166251/127‑1 (MQ=255)
                                                                                                                                   aCCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGcc                                   >  8:166251/1‑127 (MQ=255)
                                                                                                                                       tGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGAAGTACTGGCCGCCACCAGc         >  7:42741/1‑149 (MQ=255)
                                                                                                                                        gTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGAAGTACTGGCCGCCACCAg          <  7:276233/147‑1 (MQ=255)
                                                                                                                                              ccgGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTgg                                                        <  7:18773/95‑1 (MQ=255)
                                                                                                                                              ccgGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTgg                                                        >  8:18773/1‑95 (MQ=255)
                                                                                                                                              ccgGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGAAGTACTGGCCGCCACCAGCCATCTGc  <  6:370691/149‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                                 
CCGACGTCGGCAGCGCCAAGGGCAACGTCGTGCGTGAGGCGCGTGCCGTCTTCGGTGCCCGCCTGCCGCGCTTCGTCCCGGGCCACCCCATCGCCGGTTCCGAGCAGAGCGGGGTAGAGGCGTCCAATGCCACCTTGTTCCGCCGGCACAAGGTCATCCTCACGCCGCTGGCCGAAACCGACCCCGCCGCGCTGGTCCTGGTTGACCGCCTG‑TGGCGTGCGCTGGACGCCGATGTGGAGCACATGTCGGTCGAGCGCCATGACGAAGTACTGGCCGCCACCAGCCATCTGC  >  NC_002947/1976647‑1976937

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑