Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,532,699 T→C 8.1% M162V (ATG→GTG)  PP_3121 ← transcriptional regulator, LysR family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,532,6990TC 8.1% 135.8 / 2.6 49M162V (ATG→GTG) PP_3121transcriptional regulator, LysR family
Reads supporting (aligned to +/- strand):  ref base T (20/25);  new base C (2/2);  total (22/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

GGCCGCCACATTCTGCTCCATCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCACGTCGTGCACCGTGACGTTGACCTTGGGGTAGCGCTGGCGAAAC  >  NC_002947/3532553‑3532847
                                                                                                                                                  |                                                                                                                                                     
ggCCGCCACATTCTGCTCCATCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCATCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACTAAGCGGTCCATGt                                                                                                                                                     <  8:25370/149‑1 (MQ=255)
ggCCGCCACATTCTGCTCCATCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGt                                                                                                                                                     <  1:172997/149‑1 (MQ=255)
         aTTCTGCTCCATCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGt                                                                                                                                            <  4:151862/149‑1 (MQ=255)
          ttCTGCTCCATCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTg                                                                                                                                           <  8:239107/149‑1 (MQ=255)
              gcgatctCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCTAGGGCGAGTCGGCGGCCACTACGGCAAGGAAGCGGTCCACGTACAACGGGTGGaa                                                                                                                                        <  5:313826/142‑1 (MQ=255)
               cTCCATCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGaa                                                                                                                                        <  5:308326/147‑1 (MQ=255)
                  cATCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAGATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGaa                                                                                                                                        <  7:265640/144‑1 (MQ=255)
                  cATCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAGATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGaa                                                                                                                                        >  8:265640/1‑144 (MQ=255)
                  cATCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑c                                                                                                                                    <  2:163324/147‑1 (MQ=255)
                    tCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGc                                                                                                                                <  2:48232/149‑1 (MQ=255)
                      agcagGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCACGTACAACGGGTGGaa                                                                                                                                        <  5:318800/140‑1 (MQ=255)
                      agcagGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCACGTACAACGGGTGGaa                                                                                                                                        >  6:318800/1‑140 (MQ=255)
                      agcagGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTCCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCACGTACAACGGGTCGaa                                                                                                                                        >  6:313826/1‑140 (MQ=255)
                            cgcACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGAt                                                                                                                        <  1:34897/149‑1 (MQ=255)
                            cgcACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGAt                                                                                                                        <  4:227631/149‑1 (MQ=255)
                               aCCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGtt                                                                                                                     >  6:52620/1‑149 (MQ=255)
                                ccgccgAAGGGCGCTGCAGGGCCACGAAATCTACGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCTGCGGCCACTACGGCAACGAAGCGGGCCATGTACAACGGGTGGAAGT‑CCAGCCCAACCATGtt                                                                                                                     >  7:102416/1‑148 (MQ=255)
                                  gccgAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCTGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGTAAGT‑CCAGCCCATCGATGTTATc                                                                                                                  <  3:300379/149‑1 (MQ=255)
                                  gccgAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATc                                                                                                                  >  8:314867/1‑149 (MQ=255)
                                         ggCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTc                                                                                                            >  8:146827/1‑148 (MQ=255)
                                             cTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGc                                                                                                       >  5:20098/1‑149 (MQ=255)
                                             cTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGc                                                                                                       <  6:20098/149‑1 (MQ=255)
                                                  gggCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATg                                                                                                  >  8:203914/1‑149 (MQ=255)
                                                       aCGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAg                                                                                             >  6:2173/1‑149 (MQ=255)
                                                               ttCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGAcgc                                                                                     >  8:167010/1‑149 (MQ=255)
                                                                 cGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGAcgcg                                                                                    <  8:21596/148‑1 (MQ=255)
                                                                  ggCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACgcgg                                                                                   <  6:179363/148‑1 (MQ=255)
                                                                      aTCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATg                                                                              <  2:201892/149‑1 (MQ=255)
                                                                           cTGTACCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGt                                                                                                                                                     <  7:100697/74‑1 (MQ=255)
                                                                           cTGTACCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGt                                                                                                                                                     >  8:100697/1‑74 (MQ=255)
                                                                            tgtgCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTAc                                                                        >  2:217851/1‑149 (MQ=255)
                                                                              tgCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTAc                                                                        <  7:314867/147‑1 (MQ=255)
                                                                                    gCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCt                                                                <  7:146827/149‑1 (MQ=255)
                                                                                        aCCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCCTCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTAc                                                            >  2:238055/1‑149 (MQ=255)
                                                                                          cTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCt                                                          >  5:222217/1‑149 (MQ=255)
                                                                                                cagcagTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGt                                                    >  3:294227/1‑149 (MQ=255)
                                                                                                 agcagTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGtt                                                   <  6:222217/149‑1 (MQ=255)
                                                                                                 agcagTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGtt                                                   <  6:125668/149‑1 (MQ=255)
                                                                                                    agTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGAt                                                >  3:152611/1‑149 (MQ=255)
                                                                                                         cAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCAcgt                                           >  7:171136/1‑149 (MQ=255)
                                                                                                          aaGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCAcgtc                                          <  7:167010/149‑1 (MQ=255)
                                                                                                                gagtgcgcggcCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCGAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCACGTCGTGCAc                                    <  7:254161/143‑1 (MQ=255)
                                                                                                                         gcCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCACGTCGTGCACCGTGACGtt                           <  4:294227/149‑1 (MQ=255)
                                                                                                                           cACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCACGTCGTGCACCGTGACGTTGa                         <  5:2173/149‑1 (MQ=255)
                                                                                                                                 ggCAACGAAGCGGTCCATGTACAACGGGTGGAAGTGCCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCACGTCGTGCACCGTGACGTTGACCTTg                    >  1:222544/1‑149 (MQ=255)
                                                                                                                                 ggCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCACGTCGTGCACCGTGACGTTGACCTTgg                   <  8:171136/149‑1 (MQ=255)
                                                                                                                                   cAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCACGTCGTGCACCGTGACGTTGACCTTgggg                 >  4:1889/1‑149 (MQ=255)
                                                                                                                                       gAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCACGTCGTGCACCGTGACGTTGACCTTGGGGTAgc             >  3:94837/1‑149 (MQ=255)
                                                                                                                                               ccATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCACGTCGTGCACCGTGACGTTGACCTTGGGGTAGCGCTGGCg      >  1:191320/1‑148 (MQ=255)
                                                                                                                                                  tGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCACGTCGTGCACCGTGACGTTGACCTTGGGGTAGCGCTGGCGAAac  <  3:1889/149‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                                     
GGCCGCCACATTCTGCTCCATCAGCAGGCGCACCGCCGAAGGGCGCTGCAGGGCCACGAAATCTTCGGCCATCAGCTGTGCCCAGCTGACCTGGGGCAGCAGTGCCAAGGGCGAGTCGGCGGCCACTACGGCAACGAAGCGGTCCATGTACAACGGGTGGAAGT‑CCAGCCCATCGATGTTATCCGGCTCGAAGCCGATGCCCAGTTCGACGCGGCGATGGCGTACCAGTTCCTGTACCTGTTCGTTGATCACGTCGTGCACCGTGACGTTGACCTTGGGGTAGCGCTGGCGAAAC  >  NC_002947/3532553‑3532847

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: ‑