Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,639,575 C→T 10.0% intergenic (‑165/‑146) czcR‑III ← / → PP_1439 response regulator/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,639,5750CT10.0% 133.1 / 5.3 50intergenic (‑165/‑146)czcR‑III/PP_1439response regulator/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (24/21);  new base T (2/3);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 6.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.18e-01

AAGGGGACGATTCTTGACCCTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGAT  >  NC_002947/1639430‑1639722
                                                                                                                                                   |                                                                                                                                                   
atgtggACGATTCTTGTCGCTGTAGTGACATCAGGGGGAAGCGCCGCAATGTTACGGCATT‑AAAAAAGGCCTGCGGTTCAGAAAA‑CGGATTTGTAAATCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCcgctc                                                                                                                                                   <  2:214312/144‑3 (MQ=255)
  ggggACGATTCTTGACCCTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTg                                                                                                                                                >  2:23019/1‑149 (MQ=255)
     gACGATTCTTGACCCTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAg                                                                                                                                             >  7:240175/1‑149 (MQ=255)
     gACGATTCTTGACCCTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAg                                                                                                                                             >  2:254418/1‑149 (MQ=255)
            cTTGACCCTGATGTCACTACAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACggg                                                                                                                                      >  5:198697/1‑149 (MQ=255)
             ttGACCCTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGAT‑A‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGtt                                                                                                                                    >  7:106482/1‑149 (MQ=255)
               gACCCTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATGAAAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGt                                                                                                                                     <  6:55884/148‑1 (MQ=255)
               gACCCTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTACGCGAGTAAACCCGCGCCTGTAGGAACggg                                                                                                                                      <  1:23019/146‑1 (MQ=255)
                   cTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGGGTAAACCCGTTCCTACAGGCGCGGGTTTActc                                                                                                                               <  8:96432/149‑3 (MQ=37)
                   cTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTAccc                                                                                                                               >  2:75646/1‑149 (MQ=255)
                      tAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGGGTAAACCCGTTCCTACAGGCGCGGGTTTACTcg                                                                                                                              <  5:222347/147‑1 (MQ=37)
                      tAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCGGTAGGAACGGGTTTACCcgc                                                                                                                             >  4:204315/1‑148 (MQ=255)
                           aCATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAagag                                                                                                                       <  1:254418/149‑1 (MQ=255)
                              tCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGTTCCTACAGGCGCGGGTTTAc                                                                                                                                 <  8:239048/136‑1 (MQ=37)
                              tCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGTTCCTACAGGCGCGGGTTTAc                                                                                                                                 >  7:239048/1‑136 (MQ=37)
                                  ggTCACGCGCCCCAATGTTACGTCAGC‑AAAAAAGGCCTGCGGTGCAGATAA‑CGTTTTTGTAATTCTGCTTTTATCTGGCTGTCTGTGCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGaa                                                                                                                <  8:217576/149‑1 (MQ=255)
                                           ccccAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTg                                                                                                                                                <  6:266258/108‑1 (MQ=255)
                                           ccccAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTg                                                                                                                                                >  5:266258/1‑108 (MQ=255)
                                              cAATGTTACGGCATG‑AAAAACGCCCGGCGGTGCATATAA‑CGGATTTGTAATTCTGCTGTTATCGGGCTGGCTGTGCGGGCCTCTTCGCGAGTAACCCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACaa                                                                                                    <  8:57892/149‑1 (MQ=255)
                                               aaTGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGTCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGaa                                                                                                                          <  5:276582/126‑1 (MQ=255)
                                               aaTGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGaa                                                                                                                          >  6:276582/1‑126 (MQ=255)
                                                aTGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAgg                                                                                                  <  4:62765/149‑1 (MQ=255)
                                                       ggCATG‑AAAAAAGGCCTGCGGTGCAGATAANCGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCAACACAAGGc                                                                                                 >  1:24510/1‑144 (MQ=255)
                                                       ggCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGc                                                                                                 <  2:24510/143‑1 (MQ=255)
                                                          aTG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTg                                                                                          >  8:25208/1‑147 (MQ=255)
                                                                           ggTGCAGATAA‑CGGATTTGTAATTCGGGTGTTTTCTGGCTGTCTGTTCGGGCGTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTTCCCGCGAATAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGc                                                                        <  2:222205/149‑1 (MQ=255)
                                                                             tGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGc                                                                                         >  8:83525/1‑130 (MQ=255)
                                                                               cAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCa                                                                    <  8:240175/149‑1 (MQ=255)
                                                                                aGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGc                                                                                                                     >  6:140263/1‑99 (MQ=255)
                                                                                aGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGc                                                                                                                     <  5:140263/99‑1 (MQ=255)
                                                                                aGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCAc                                                                   >  7:80271/1‑149 (MQ=255)
                                                                                   tAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCtt                                                                >  3:94202/1‑149 (MQ=255)
                                                                                     a‑CGGATTTGTAATGCTGCTGTAATCTGGCTGGCTGTTCGGGCCTCTGCGCGAGTAAACCCGCGCCTGTAGGACCGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGc                                                              <  3:127047/149‑1 (MQ=255)
                                                                                        ggATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTAGCGAGTTAAACCGCGGCTGTAGGAACGGGTTTACACGCGAAGAGGCCCGAACAGTGCACACAAGGCCACAATGCAGGACAGTTATACCCGCCTAACCTTGCCg                                                            >  6:26208/1‑149 (MQ=255)
                                                                                                        tgTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCACCGCCTCACCTTCCCGTTAGACAGCCCTCGc                                             >  4:40207/1‑148 (MQ=255)
                                                                                                             tCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGAt                                       >  6:119273/1‑149 (MQ=255)
                                                                                                                     tctgtTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCgtgt                               <  7:25208/149‑1 (MQ=255)
                                                                                                                     actgtTCGGGCCTCTTCGCGGGTAAACCCGTTCCTACAGGCGCGGGTTTACCCGCGAAGAGGCCCGCACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCACGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCgtgt                               >  8:60964/2‑149 (MQ=21)
                                                                                                                         ttCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGGACGGGGTTACCCGCGAAGAGGCCCGAACAGTCCCCCCAAGGCCCCCTTGCAGGCCTGTAATCCCCGCCTCACCTTGCCGTTAGCCCGCCCTCGCGAGGCTGGCCGTGGCTGa                           >  3:226205/1‑149 (MQ=37)
                                                                                                                           cGGCCCTCTACGCGAGTAAACCCCCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGAt                          <  3:204315/148‑1 (MQ=255)
                                                                                                                            gggCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCg                        <  4:94202/149‑1 (MQ=255)
                                                                                                                             ggCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCgg                       >  4:98602/1‑149 (MQ=255)
                                                                                                                                ctctTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCgtgt                               <  3:88949/138‑1 (MQ=255)
                                                                                                                                ctctTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCgtgt                               >  4:88949/1‑138 (MQ=255)
                                                                                                                                  ctTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGttat                   >  1:127517/1‑148 (MQ=255)
                                                                                                                                      gcgAGTAAACCCGCGCCTGTAGGAAGGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGa              <  4:226205/149‑1 (MQ=255)
                                                                                                                                       cgAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAg             <  3:98602/149‑1 (MQ=255)
                                                                                                                                            aaaCCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCaaa        >  4:53089/1‑149 (MQ=255)
                                                                                                                                                ccGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTagcca                                                     <  8:21344/100‑1 (MQ=255)
                                                                                                                                                ccGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTagcca                                                     >  7:21344/1‑100 (MQ=255)
                                                                                                                                                ccGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACg    <  5:119273/149‑1 (MQ=255)
                                                                                                                                                  gcgcCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGAt  <  1:75646/149‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                   
AAGGGGACGATTCTTGACCCTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGAT  >  NC_002947/1639430‑1639722

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑