Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,556,609 C→T 8.3% G81S (GGC→AGC)  rtcA ← RNA 3'‑terminal phosphate cyclase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,556,6090CT 8.3% 109.2 / 2.1 49G81S (GGC→AGC) rtcARNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base C (23/22);  new base T (2/2);  total (25/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.50e-01

GACGGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGCCCCGGTTTCGCCCGCCCGGCACGAATGCTGGTGA  >  NC_000913/3556467‑3556746
                                                                                                                                              |                                                                                                                                         
gACGGGTTATCGGTGCCGCCGCTCACTCCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTgcc                                                                                                                                           <  2:679927/143‑1 (MQ=255)
     gTTAGCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTCCCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTgccgggcc                                                                                                                                      <  1:203464/143‑1 (MQ=255)
      ttATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATGGGCAAACCACAGCGCGGGCAGCACCGTTTGCCGCAGCAGCGCACAACTTCAGGCGCTAACGATAGCAAAGCGGTAATGGCCGCCGCGCACGCTgcccggccg                                                                                                                                     >  2:676786/1‑143 (MQ=255)
      ttATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAACGCGGTAATCGCCGCCGCGCACGGTgccgggccg                                                                                                                                     >  1:455881/1‑143 (MQ=255)
         tCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCCGTAATCGCCGCCGCGCACGGTGCCGGTCCGTaa                                                                                                                                  >  1:945577/1‑143 (MQ=255)
            gTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCAAAGCGCGGGCAGCACCGTTTGCAGCGCCAGCGTACAACTTCCGGCGCTACCGCTAGCAAGGCGGTAATCGCTGCCGCGCGCGCTGCCGGGCCGGCagcg                                                                                                                               >  2:60905/1‑141 (MQ=255)
             tGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGc                                                                                                                              <  1:857431/143‑1 (MQ=255)
               ccgccgCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCCGTAATCGCCGCCGCGCACGGCGCCGGGCCGGCAGAGccg                                                                                                                            >  2:199517/1‑141 (MQ=255)
                          ttCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGAcc                                                                                                                 >  1:390466/1‑143 (MQ=255)
                              acacGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGGGACCCCAg                                                                                                             >  1:986521/1‑143 (MQ=255)
                               cacGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCTGGGCCGGAAGAGCAGACGCTGCGACCCCAGc                                                                                                            >  2:454903/1‑143 (MQ=255)
                               cacGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCTGGGCCGGAAGAGCAGACGCTGCGACCCCAGc                                                                                                            >  2:1004574/1‑143 (MQ=255)
                                   cgAAGGTCCACCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCcg                                                                                                        <  1:363624/143‑1 (MQ=255)
                                    gAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAGCTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCcgc                                                                                                       <  2:677058/143‑1 (MQ=255)
                                    gAAGGGCCATCCGCAAACCACAGCTCGGGCAGCACCGTTTGCACCACCAGCCTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCcgc                                                                                                       <  1:1047877/143‑1 (MQ=255)
                                        gTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCcgcggcg                                                                                                   >  2:125191/1‑140 (MQ=255)
                                         tCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCtt                                                                                                  <  2:720542/143‑1 (MQ=255)
                                                gCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGGAATCGCCGCCGCGCCCGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCGTGCACGGt                                                                                           >  2:128518/1‑143 (MQ=255)
                                                 cAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGtt                                                                                          >  1:808656/1‑143 (MQ=255)
                                                  aaaCCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGGAATCGCCGCCGCGCACGGTGCCGGGCCGGAACAGCAGACGCCGCGACGCCAGCGCCGCGCCATCAAccattg                                                                                         >  2:212246/1‑138 (MQ=255)
                                                   aaCCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAGTCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCGTCCACGGCTGc                                                                                        >  2:653190/1‑143 (MQ=255)
                                                    aCCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCt                                                                                       >  1:233092/1‑143 (MQ=255)
                                                      cacaGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGACGACGACACGACCCCAGCTCCGCGCCTTCCACCGCTGcccc                                                                                     >  2:1029020/1‑143 (MQ=255)
                                                                gcagcaCCGTTTGCAGCACGAGCGTACATCTTTCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTcc                                                                           <  2:187449/143‑1 (MQ=255)
                                                                gcagcaCCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAGTTTcc                                                                           >  1:329494/1‑143 (MQ=255)
                                                                      ccGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCCGCTCCGCGCCTTCCACGGTCGCTCCGCCACTTTCCGTcgcc                                                                     >  2:246710/1‑143 (MQ=255)
                                                                             cagcaCCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCTGTAATTGTTGCGCATTCCGACTCCTGTCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTa                                                              <  1:242113/143‑1 (MQ=255)
                                                                             cagcaCCAGCGTACAACTCCCGGCGCTACGGACAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTa                                                              <  2:881508/143‑1 (MQ=255)
                                                                                caCCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAAGCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACcg                                                           <  2:989015/143‑1 (MQ=255)
                                                                                caCCAGCGTACAACTGCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACcg                                                           <  1:939801/143‑1 (MQ=255)
                                                                                   cAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGCAGAGCAGACGCTGCGACCCCCGCTCCGCGCCTTCCACGGGCGCCCCGCAACCTTCCGTCGCCGCCTTTACCCCgg                                                        >  2:69462/1‑143 (MQ=255)
                                                                                        tACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCCCGCTCAGa                                                   >  2:259621/1‑143 (MQ=255)
                                                                                              ggccGGCGGGACCGAGAGCAAAGCGGGAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTgg                                             <  2:297854/141‑1 (MQ=255)
                                                                                                   gcgcGACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCTCaa                                        <  1:836008/143‑1 (MQ=255)
                                                                                                         ccGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGGTGCTCCGCAAATTTCCGTCGCCGCCTTTCCCGCGGTCAGACGCTGGCGCAACAGccc                                  >  2:527085/1‑143 (MQ=255)
                                                                                                          cgttAGCAAACCGTTATTCGCCGCCGCGCACGGTGCCGGGCCGGTCGAGCAGACGCTGCGACCCCAGCGCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGcccc                                 <  2:65139/140‑1 (MQ=255)
                                                                                                          cGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGcccc                                 <  2:831757/143‑1 (MQ=255)
                                                                                                            aTAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCTGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGCCCCgg                               <  1:1004574/143‑1 (MQ=255)
                                                                                                            aTAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCTGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGCCCCgg                               <  1:454903/143‑1 (MQ=255)
                                                                                                            aTAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAAttt                                                                             >  1:860712/1‑97 (MQ=255)
                                                                                                            aTAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAAttt                                                                             <  2:860712/97‑1 (MQ=255)
                                                                                                                cAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGGCGTCGACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCCGATGCAGGCGCAACCGCCCCGGttgc                           >  2:15096/1‑141 (MQ=255)
                                                                                                                cAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGGCAGATGCTGGCGCCACCGCCCCGGTTTc                           >  1:1045177/1‑143 (MQ=255)
                                                                                                                      tgtatttgccgccgcGCACCGTGCCGCGCCGGCAGAGCACACGCTGCGACCCCCGCTCCGCGCCTCCCACGGTCGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGACAGATGCTGGCGCAACAGCCCCGGTTTcgcccgc                     <  2:623743/136‑1 (MQ=255)
                                                                                                                       gTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGATGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGCCCCGGTTTcgcccgcc                    >  2:1049297/1‑143 (MQ=255)
                                                                                                                         actCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGCCCCGGTTTCGcccgcccg                  <  1:846818/141‑1 (MQ=255)
                                                                                                                           tCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGCCCCGGTTTCGCCCGCCCGGc                <  2:808656/143‑1 (MQ=255)
                                                                                                                                   gcgcACGGTGCCGGGCCGGCAGCGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGCCCCGGTTTCGCCCGCCCGGCACGAATGc        <  1:653190/143‑1 (MQ=255)
                                                                                                                                     ggaCGGCGCCGGGCCGGAACAGCAGACGCCGCGACCCCAGCTCCGCGCCTTCCACGGTTGCCCCGCAACTTTCCGTCGCCGCCTTTACCGCGGGCAGATGCTGGCGCAACAGCCCCGGTTTCGCCCGCCCGGCACGAATGCTg      <  2:68574/141‑1 (MQ=255)
                                                                                                                                     gcACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGCCCCGGTTTCGCCCGCCCGGCACGAATGCTg      <  1:923284/143‑1 (MQ=255)
                                                                                                                                      cACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGGGCAACAGCCCCGGTTTCGCCGGCACGGCAGGaagggggg     >  2:356459/1‑137 (MQ=255)
                                                                                                                                       aCGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGCCCCGGTTTCGCCCGCCCGGCACGAATGCTGGt    >  2:399942/1‑143 (MQ=255)
                                                                                                                                         ggTGCCGGGCCGGAAGAGCGGACGCTGCGACCCCTGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGCCCCGGTTTCGCCCGCCCGGCACGAATGCTGGTGa  <  2:1028149/143‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                         
GACGGGTTATCGGTGCCGCCGCTCACTTCAACACGCGAAGGTCCATCGGCAAACCACAGCGCGGGCAGCACCGTTTGCAGCACCAGCGTACAACTTCCGGCGCTACCGATAGCAAAGCGGTAATCGCCGCCGCGCACGGTGCCGGGCCGGAAGAGCAGACGCTGCGACCCCAGCTCCGCGCCTTCCACGGTTGCTCCGCAAATTTCCGTCGCCGCCTTTACCGCGGTCAGATGCTGGCGCAACAGCCCCGGTTTCGCCCGCCCGGCACGAATGCTGGTGA  >  NC_000913/3556467‑3556746

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑