Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,639,586 A→G 9.9% intergenic (‑176/‑135) 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_0029471,639,5860AG 9.9% 130.7 / 5.5 51intergenic (‑176/‑135)czcR‑III/PP_1439response regulator/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (21/24);  new base G (2/3);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.18e-01

CTTGACCCTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGATGAACCTGACCA  >  NC_002947/1639442‑1639733
                                                                                                                                                  |                                                                                                                                                   
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)
                                  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                                          >  4:88949/1‑138 (MQ=255)
                                                                                                                    ctctTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCgtgt                                          <  3:88949/138‑1 (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                                                                >  7:21344/1‑100 (MQ=255)
                                                                                                                                    ccGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTagcca                                                                <  8:21344/100‑1 (MQ=255)
                                                                                                                                    ccGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACg               <  5:119273/149‑1 (MQ=255)
                                                                                                                                      gcgcCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGAt             <  1:75646/149‑1 (MQ=255)
                                                                                                                                        gcCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGATGa           <  3:40207/149‑1 (MQ=255)
                                                                                                                                            gTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGATGAACCt       >  4:247093/1‑149 (MQ=255)
                                                                                                                                             tAGGAACGGTTTTACCCGCTAAGAGGCACTAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGATGAAcc        <  7:104966/147‑1 (MQ=255)
                                                                                                                                             tAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGATGAAcc        <  8:106482/147‑1 (MQ=255)
                                                                                                                                             tAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGATGAACCt       <  2:28078/148‑1 (MQ=255)
                                                                                                                                                  aCGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGTCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGATGAACCTGACCa  >  8:22277/1‑148 (MQ=255)
                                                                                                                                                  |                                                                                                                                                   
CTTGACCCTGTAGTGACATCAGGGTCAAGCGCCCCAATGTTACGGCATG‑AAAAAAGGCCTGCGGTGCAGATAA‑CGGATTTGTAATTCTGCTGTTATCTGGCTGTCTGTTCGGGCCTCTTCGCGAGTAAACCCGCGCCTGTAGGAACGGGTTTACCCGCGAAGAGGCCCGAACAGTCCACACAAGGCCACATTGCAGGACTGTAATCCCCGCCTCACCTTGCCGTTAGCCAGCCCTCGCTAGGATGGCCGTGTCTGATCGGTTATTACGAGGCAAACACGATGAACCTGACCA  >  NC_002947/1639442‑1639733

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: ‑