Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,103,888 A→C 7.8% E139A (GAA→GCA)  PP_2714 → sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,103,8880AC 7.8% 154.3 / 4.5 51E139A (GAA→GCA) PP_2714sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base A (21/26);  new base C (2/2);  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 = 9.70e-01

ATTCCAGGTCTGGGGTGAAGGCATGGCGTTGCTGGTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGATCGGCTGGGGGCTGCGG  >  NC_002947/3103745‑3104036
                                                                                                                                               |                                                                                                                                                    
aTTCCAGGTCTGGGGTGAAGGCATGGCGTTGCTGGTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGaaaaa                                                                                                                                                  >  1:137838/1‑148 (MQ=255)
aTTCCAGGTCTGGGGTGAAGGCATGGCGTTGCTGGTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGaaaaa                                                                                                                                                  >  8:74403/1‑148 (MQ=255)
 ttCCAGGTCTGGGGTGAAGGCATGGCGTTGCTGGTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAaca                                                                                                                                                <  8:134816/149‑1 (MQ=255)
    cAGGTCTGGGGTGAAGGCATGGTGTTGCTGGTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTCGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACt                                                                                                                                              <  1:132109/148‑1 (MQ=255)
    cAGGTCTGGGGTGAAGGCATGGCGTTGCTGGTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTg                                                                                                                                             >  1:196304/1‑149 (MQ=255)
    cAGGTCTGGGGTGAAGGCATGGCGTTGCTGGTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTg                                                                                                                                             >  4:269517/1‑149 (MQ=255)
    cAGGTCTGGGGTGAAGGCATGGCGTTGCTGGTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTg                                                                                                                                             <  3:269517/149‑1 (MQ=255)
                   ggCATGGCGTTGCTGGTGTATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCtgggtggg                                                                                                                              <  7:49534/149‑1 (MQ=255)
                      aTGGCGTTGCTGGTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTg                                                                                                                                             >  8:58109/1‑131 (MQ=255)
                      aTGGCGTTGCTGGTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTg                                                                                                                                             <  7:58109/131‑1 (MQ=255)
                           gTTGCTGGTGGATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGtg                                                                                                                      >  3:19978/1‑149 (MQ=255)
                                  gTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTgatgat                                                                                                                 <  1:269162/147‑1 (MQ=255)
                                  gTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTgatgat                                                                                                                 <  7:74403/147‑1 (MQ=255)
                                   tGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGAtgtg                                                                                                              >  4:173695/1‑149 (MQ=255)
                                     cATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTgc                                                                                                             <  4:19978/148‑1 (MQ=255)
                                     cATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATATGGGTGGGGGAGCGTGATGATGTgcg                                                                                                            >  2:172785/1‑149 (MQ=255)
                                            ccAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCt                                                                                                          <  7:212047/144‑1 (MQ=255)
                                            ccAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCt                                                                                                          >  8:212047/1‑144 (MQ=255)
                                            ccAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGAc                                                                                                     >  3:155846/1‑149 (MQ=255)
                                                                       ccacTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGATCAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCt                                                                                                   <  4:254943/124‑1 (MQ=255)
                                                                       ccacTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGATCAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCt                                                                                                   >  3:254943/1‑124 (MQ=255)
                                                                        cacTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGc                                                                         >  6:227933/1‑149 (MQ=255)
                                                                         acTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCt                                                                        >  1:177421/1‑149 (MQ=255)
                                                                             cTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTc                                                                    >  8:209464/1‑149 (MQ=255)
                                                                              tCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTcc                                                                   >  7:19701/1‑149 (MQ=255)
                                                                              tCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTcc                                                                   >  6:128431/1‑149 (MQ=255)
                                                                                cAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCtt                                                                                                                                         >  7:155846/1‑77 (MQ=255)
                                                                                cAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCtt                                                                                                                                         <  8:155846/77‑1 (MQ=255)
                                                                                        tACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCt                                                         >  3:109368/1‑149 (MQ=255)
                                                                                          cGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCtt                                                        <  4:155846/148‑1 (MQ=255)
                                                                                             cTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCa                                                    <  2:177421/149‑1 (MQ=255)
                                                                                                     gTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCg                                            >  3:237956/1‑149 (MQ=255)
                                                                                                        gCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGtt                                          <  4:109368/148‑1 (MQ=255)
                                                                                                               aCAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCActgc                                  <  2:137838/149‑1 (MQ=255)
                                                                                                                 aaTGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTgg                                                      <  2:153017/127‑1 (MQ=255)
                                                                                                                 aaTGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTgg                                                      >  1:153017/1‑127 (MQ=255)
                                                                                                                        cgGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTggg                         <  5:227933/149‑1 (MQ=255)
                                                                                                                        cgGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTggg                         <  4:325918/149‑1 (MQ=255)
                                                                                                                          ccagtgTTTTTCCGGCACCGGCAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGgtgt                            <  5:246771/139‑1 (MQ=255)
                                                                                                                          ccagtgTTTTTCCGGCACCGGCAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGgtgt                            >  6:246771/6‑144 (MQ=255)
                                                                                                                               gTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCCGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGAt                  >  4:84746/1‑149 (MQ=255)
                                                                                                                               gTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGa                   <  5:128431/148‑1 (MQ=255)
                                                                                                                               gTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGAt                  <  4:237956/149‑1 (MQ=255)
                                                                                                                                ttttTCCGGCACCGGCAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGATc                 >  3:181316/1‑149 (MQ=255)
                                                                                                                                      cggcaccggCAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGATCGGCTg            <  4:181316/143‑1 (MQ=255)
                                                                                                                                      cggagccggAAAAACACTGGCTTATCTGGGCGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGGGTGGGCTGCGATCGGCTgg           <  4:122225/149‑1 (MQ=255)
                                                                                                                                       ggtgccggAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCGGGTGTGGGCTGCGATCGGCTggg          <  1:172785/149‑1 (MQ=255)
                                                                                                                                        gtgccggAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCACATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGATCGGCTgggg         <  2:196304/149‑1 (MQ=255)
                                                                                                                                         tgccggAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGATCGGCTggggg        <  3:173695/149‑1 (MQ=255)
                                                                                                                                             ggAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGATCgg               >  1:67048/1‑138 (MQ=255)
                                                                                                                                             ggAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGATCgg               <  2:67048/138‑1 (MQ=255)
                                                                                                                                              gAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCActgct                                 <  4:243753/119‑1 (MQ=255)
                                                                                                                                              gAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCActgct                                 >  3:243753/1‑119 (MQ=255)
                                                                                                                                               aaaaaCACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGATCGGCTGGGGGCTGCgg  >  6:324501/1‑149 (MQ=255)
                                                                                                                                               |                                                                                                                                                    
ATTCCAGGTCTGGGGTGAAGGCATGGCGTTGCTGGTGCATACACCCAGTGCGCCACCCATCGACCCACCACCCACTGCTCCAGGGTTCTACGACTTTTCCAGTGGCGGTGAACAATGGCGCGGTTTCGTTTTGCCGGTGCCGGAAAAACACTGGCTTATCTGGGTGGGGGAGCGTGATGATGTGCGCTACGACCTGATCGACCGCATCGTTCGCCACACGCTGTTCCCGTTCCTGCTTGGCAGCCTGGCGTTGGCACTGCTGGTGTGGGCTGCGATCGGCTGGGGGCTGCGG  >  NC_002947/3103745‑3104036

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: ‑