Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,698,114 T→C 10.4% M716T (ATG→ACG)  PP_1492 → two‑component system sensor histidine kinase/response regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,698,1140TC10.4% 96.1 / 2.5 38M716T (ATG→ACG) PP_1492two‑component system sensor histidine kinase/response regulator
Reads supporting (aligned to +/- strand):  ref base T (17/17);  new base C (2/2);  total (19/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01

CGGTGGATGGCATGGACGGCTGGAACGCCCTGCGCAGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCGGAGTTGCTCAGGGATGAAGATC  >  NC_002947/1697970‑1698261
                                                                                                                                                |                                                                                                                                                   
cggtggATGGCATGGACGGCTGGAACGCCCTGCGCAGTGAGGACTTCTACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGAtggtg                                                                                                                                                 <  6:270120/149‑1 (MQ=255)
 ggtggATGGCATGGACGGCTGGAACGCCCTGCGCAGTGAGGACTTCGACCTGTTGATCACCGCCATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCATCACCGGCAATGACTGCAGGCGCtggtcg                                                                                                                                                <  4:236117/149‑3 (MQ=255)
  gtggATGGCATGGACGGCTGGAACGCCCTGCGCAGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATggtggt                                                                                                                                               <  2:189854/149‑1 (MQ=255)
        ggCATGGACGGCTGGAACGCCCTGCGCAGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCt                                                                                                                                          <  3:11000/148‑1 (MQ=255)
         gCATGGACGGCTGGAACGCCCTGCGCAGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCtat                                                                                                                                        <  7:175024/149‑1 (MQ=255)
             ggACGGCTGGAACGCCCTGCGCAGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCtata                                                                                                                                       >  3:149708/1‑146 (MQ=255)
                     ggAACGCCCTGCGCAGGGACGACATCGACCTGTTGATCACCGACATCGACATGCCGCGCAAGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAg                                                                                                                            <  8:289607/149‑1 (MQ=255)
                        aCGCCCTGCGCAGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAgg                                                                                                                           >  2:78216/1‑147 (MQ=255)
                         cGCCCTGCGCAGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGAtggtg                                                                                                                                                 >  4:285625/1‑124 (MQ=255)
                         cGCCCTGCGCAGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGAtggtg                                                                                                                                                 <  3:285625/124‑1 (MQ=255)
                           cccTGCGCAGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGAc                                                                                                                      >  6:322559/1‑149 (MQ=255)
                                   aGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCta                                                                                                                                         <  8:111478/122‑1 (MQ=255)
                                   aGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCta                                                                                                                                         >  7:111478/1‑122 (MQ=255)
                                          aCTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTg                                                                                                       <  6:202342/149‑1 (MQ=255)
                                            ttCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGa                                                                                                     >  4:179134/1‑149 (MQ=255)
                                                          cACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGac                                                                                        >  3:328041/1‑148 (MQ=255)
                                                                 atcgacatGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGACGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTAttt                                                                                >  1:140904/1‑149 (MQ=255)
                                                                 atcgacatGCCGCGCATGGACGGTATCGAGCTGGTTACCCT‑GTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTg                                                                               >  8:322645/1‑149 (MQ=255)
                                                                   cgacatGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGACGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTg                                                                               >  3:330562/1‑148 (MQ=255)
                                                                   cgacatGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGACGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTg                                                                               <  4:330562/148‑1 (MQ=255)
                                                                           cgcgCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGc                                                                       >  4:55291/1‑148 (MQ=255)
                                                                            gcgcATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGc                                                                       >  5:116861/1‑147 (MQ=255)
                                                                                        tATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTACAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCacgac                                                          >  8:11245/1‑148 (MQ=255)
                                                                                            gAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGGGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGactac                                                                                     >  4:219597/1‑117 (MQ=255)
                                                                                             aGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACAGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCg                                                    >  7:218400/1‑149 (MQ=255)
                                                                                                  gTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTAtt                                                                                 >  2:60941/1‑115 (MQ=255)
                                                                                                  gTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTAtt                                                                                 <  1:60941/115‑1 (MQ=255)
                                                                                                  gTTACCCTGGTGCGTCGCGACCAGCGCCTACAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGc                                                <  7:11245/148‑1 (MQ=255)
                                                                                                            tGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGACGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCtgtt                                     <  2:140904/149‑1 (MQ=255)
                                                                                                                tCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTgg                                 <  5:322559/149‑1 (MQ=255)
                                                                                                                  gcgACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGaa                               <  6:116861/149‑1 (MQ=255)
                                                                                                                    gACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCg                                                                                                >  2:30222/1‑82 (MQ=255)
                                                                                                                    gACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTCAGGAAGACCGACGGCGTGGCCTGGACGCCg                                                                                                <  1:30222/82‑1 (MQ=255)
                                                                                                                         gcgcCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCg                        <  1:78216/149‑1 (MQ=255)
                                                                                                                          cgcCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCgg                       <  4:149708/149‑1 (MQ=255)
                                                                                                                           gcCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCGGa                      <  3:55291/149‑1 (MQ=255)
                                                                                                                               gCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTTCTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCGGAGTTg                  <  8:218400/149‑1 (MQ=255)
                                                                                                                                 aGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCGGAGTTGCt                >  6:159592/1‑149 (MQ=255)
                                                                                                                                   tCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCGGAGTTGCTCa              <  3:179134/149‑1 (MQ=255)
                                                                                                                                     aTTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCGGAGTTGCTCAgg            >  1:338384/1‑149 (MQ=255)
                                                                                                                                      ttGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCGGAGTTGCTCAgg            >  7:172391/1‑148 (MQ=255)
                                                                                                                                         ccGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCGGAGTTGCTCAGGGATg        <  8:172391/149‑1 (MQ=255)
                                                                                                                                                tgggggTGTCCTATAAAGACCGTGAGGAAGACCTACGGCGGGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCGGAGTTGCTCAGGGATGAAGATc  <  2:338384/148‑1 (MQ=255)
                                                                                                                                                |                                                                                                                                                   
CGGTGGATGGCATGGACGGCTGGAACGCCCTGCGCAGTGAGGACTTCGACCTGTTGATCACCGACATCGACATGCCGCGCATGGACGGTATCGAGCTGGTTACCCTGGTGCGTCGCGACCAGCGCCTGCAGTCATTGCCGGTGATGGTGGTGTCCTATAAAGACCGTGAGGAAGACCGACGGCGTGGCCTGGACGCCGGCGCCGACTACTATTTGGCAAAGGCCAGTTTCCACGACGATGCGTTGCTGGATGCTGTTGTGGAACTGATCGGAGTTGCTCAGGGATGAAGATC  >  NC_002947/1697970‑1698261

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: ‑