Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,051,888 T→A 11.5% L182Q (CTG→CAG) ‡ 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_0029473,051,8880TA11.5% 148.2 / 9.0 52L182Q (CTG→CAG) ‡PP_2664two‑component system sensor histidine kinase/response regulator
Reads supporting (aligned to +/- strand):  ref base T (26/20);  new base A (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

GATGCTGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGAGCGCACTGCCG  >  NC_002947/3051745‑3052037
                                                                                                                                               |                                                                                                                                                     
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                                                                                                           <  2:694340/150‑1 (MQ=255)
                                      agcaCTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGtggtgg                                                                                                           >  1:322695/1‑150 (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                                                                                                                                                >  1:362552/1‑78 (MQ=38)
                                                                         gCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCAGCATGTAGCGTTcc                                                                                                                                                <  2:362552/78‑1 (MQ=38)
                                                                             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               >  1:1291000/1‑150 (MQ=255)
                                                                                                                                  gAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTgcgc               >  2:1146162/1‑150 (MQ=255)
                                                                                                                                         aCATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGAGCGCa        <  2:1291000/150‑1 (MQ=255)
                                                                                                                                           aTGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGAGCGCACt      >  2:1026424/1‑150 (MQ=255)
                                                                                                                                               tgcGTTCGTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGGTCCGCGAAATCACCGAGCGCCGCAACACCGTACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGTGCGCACTGCCg  <  2:534615/150‑1 (MQ=255)
                                                                                                                                               |                                                                                                                                                     
GATGCTGGGCCAGAGCCTGCGCGAGGCCCACAGCGAGCAGCACTACCAGCGCCTGGAAGGCTATGTGGCGCGGGCACTGGCGGGGGAGAGCGTGACGTTCGAGTTCGCCGAGACCAATATCAACGGCCAGGAACGCTACATGCTGCGTTCCTACGTACCGAACCGCCTGGCCAGTGGCGAAGTGGTGGGTATCTTCGTGCTGATCCGCGACATCACCGAGCGCCGCAACACCGCACAGGCGTTGCACCAGGCGTATCAGCACCTGGAGCAACGGGTGCGCGAGCGCACTGCCG  >  NC_002947/3051745‑3052037

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑