Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,051,887 C→T 11.5% L182L (CTG→TTG) ‡ PP_2664 → 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_0029473,051,8870CT11.5% 133.5 / 7.9 52L182L (CTG→TTG) ‡PP_2664two‑component system sensor histidine kinase/response regulator
Reads supporting (aligned to +/- strand):  ref base C (26/20);  new base T (3/3);  total (29/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

GATGCTGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGAGCGCACT  >  NC_002947/3051745‑3052033
                                                                                                                                              |                                                                                                                                                  
gATGCTGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTc                                                                                                                                             <  2:1236106/150‑1 (MQ=255)
    cTGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTAc                                                                                                                                         <  1:1196718/150‑1 (MQ=255)
      gggCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGt                                                                                                                                       >  2:470432/1‑150 (MQ=255)
         ccAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCAGCATGTAGCGTTCCtgg                                                                                                                                         >  2:1035903/1‑143 (MQ=255)
         ccAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCAGCATGTAGCGTTCCtgg                                                                                                                                         <  1:1035903/145‑3 (MQ=255)
         ccAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCAGCATGTAGCGTTCCtg                                                                                                                                          <  2:342834/144‑2 (MQ=255)
         ccAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCAGCATGTAGCGTTCCtg                                                                                                                                          >  1:342834/1‑143 (MQ=255)
               ccTGCGCGAGGCCCAGAAAGAGCGGCACGACCAGCACCTGTGACGGTAGTTGGGTAGGGCACTGGGGGCGGCGAATGCTACGTACGAGTTCGCCAAGACCAGTATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAAcac                                                                                                                              >  2:693987/1‑148 (MQ=255)
               ccTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGTAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCg                                                                                                                              >  1:810421/1‑150 (MQ=255)
                   cgcgAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTg                                                                                                                          <  2:729671/150‑1 (MQ=255)
                   cgcgAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTg                                                                                                                          <  1:505120/150‑1 (MQ=255)
                           ccACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGCGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTg                                                                                                                          <  1:522574/142‑1 (MQ=255)
                           ccACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTg                                                                                                                          >  2:522574/1‑142 (MQ=255)
                             acaGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAAc                                                                                                                                <  2:120392/134‑1 (MQ=255)
                             acaGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAAc                                                                                                                                >  1:120392/1‑134 (MQ=255)
                             acaGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCg                                                                                                                >  2:1138646/1‑150 (MQ=255)
                                gCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAg                                                                                                             >  1:1285042/1‑150 (MQ=255)
                                    gcagcaCTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAgtggt                                                                                                         <  1:952860/150‑1 (MQ=255)
                                     cagcaCTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAgtggtg                                                                                                        >  1:694340/1‑150 (MQ=255)
                                      agcaCTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGtggtgg                                                                                                       <  2:943642/150‑1 (MQ=255)
                                      agcaCTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGtggtgg                                                                                                       >  1:322695/1‑150 (MQ=255)
                                      agcaCTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGtggtgg                                                                                                       <  2:694340/150‑1 (MQ=255)
                                           tACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATc                                                                                                  <  1:470432/150‑1 (MQ=255)
                                           tACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATc                                                                                                  >  1:534615/1‑150 (MQ=255)
                                           tACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTACTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATc                                                                                                  >  1:661152/1‑150 (MQ=255)
                                               aGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCCTGAAATACGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCg                                                                                              <  2:399198/150‑1 (MQ=255)
                                                          ggCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACTTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCcgg                                                                                   <  1:505443/150‑2 (MQ=255)
                                                          ggCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCcgc                                                                                   >  1:1293392/1‑150 (MQ=255)
                                                                 tgGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCa                                                                            <  1:42632/150‑1 (MQ=255)
                                                                 tgGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCa                                                                            <  1:490218/150‑1 (MQ=255)
                                                                         gCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCAGCATGTAGCGTTcc                                                                                                                                            <  2:362552/78‑1 (MQ=38)
                                                                         gCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCAGCATGTAGCGTTcc                                                                                                                                            >  1:362552/1‑78 (MQ=38)
                                                                             tGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACAtgc                                                                                                                                                    <  2:67495/66‑1 (MQ=255)
                                                                             tGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACAtgc                                                                                                                                                    >  1:67495/1‑66 (MQ=255)
                                                                             tGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCa                                                                >  1:1227875/1‑150 (MQ=255)
                                                                                             gACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGtt                                                <  2:322695/150‑1 (MQ=255)
                                                                                             gACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCAGCAACACCGCACAGGCGtt                                                >  1:1187391/1‑150 (MQ=255)
                                                                                                 ttCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACAtgct                                                                                                                                                   <  1:746240/47‑1 (MQ=255)
                                                                                                 ttCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACAtgct                                                                                                                                                   >  2:746240/1‑47 (MQ=255)
                                                                                                 ttCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCGCGGGCGAAGTGGTGGGTATATTCGTGCTGACACGACGTGGCACCTAGTGCCCCAACACCGCACAGGCGGTGCAc                                            >  1:1026977/1‑150 (MQ=255)
                                                                                                        tCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGt                                     >  2:925924/1‑150 (MQ=255)
                                                                                                           ccGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGc                                       >  2:1149018/1‑145 (MQ=255)
                                                                                                           ccGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGc                                       <  1:1149018/145‑1 (MQ=255)
                                                                                                           ccGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATc                                  <  1:79280/150‑1 (MQ=255)
                                                                                                                  cAATATCAACGGCCAGGAACACTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTAGGTATCATCGTGGATATCGGCTACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGGATCAGCACCt                           >  1:101035/1‑150 (MQ=255)
                                                                                                                   aaTATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTg                          >  1:177152/1‑150 (MQ=255)
                                                                                                                          aCGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAgt                                                                                                            >  2:1298140/1‑61 (MQ=255)
                                                                                                                          aCGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAgt                                                                                                            <  1:1298140/61‑1 (MQ=255)
                                                                                                                          aCGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAAc                   >  2:879889/1‑150 (MQ=255)
                                                                                                                              ccAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGt               >  1:1345596/1‑150 (MQ=255)
                                                                                                                              ccAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGt               <  2:810421/150‑1 (MQ=255)
                                                                                                                                 ggAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTgcg            >  2:1170994/1‑150 (MQ=255)
                                                                                                                                  gAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTgcgc           >  2:1146162/1‑150 (MQ=255)
                                                                                                                                  gAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTgcgc           >  1:1291000/1‑150 (MQ=255)
                                                                                                                                         aCATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGAGCGCa    <  2:1291000/150‑1 (MQ=255)
                                                                                                                                           aTGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGAGCGCACt  >  2:1026424/1‑150 (MQ=255)
                                                                                                                                              |                                                                                                                                                  
GATGCTGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGAGCGCACT  >  NC_002947/3051745‑3052033

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑