Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,871,727 G→C 9.3% A233G (GCC→GGC)  PP_3420 ← sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,871,7270GC 9.3% 128.7 / 4.6 43A233G (GCC→GGC) PP_3420sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (21/18);  new base C (2/2);  total (23/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.42e-01

GTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCGGGATGTAGTTCTCGATGAACAGGTAGCGTGGTGCGCGCTGAAAC  >  NC_002947/3871579‑3871876
                                                                                                                                                     |                                                                                                                                                     
gtgAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGc                                                                                                                                                      >  2:775722/1‑150 (MQ=255)
     ccACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGa                                                                                                                                                 >  2:734185/1‑150 (MQ=255)
       aCTGCCGACTACATTTCACCCAGCGCAACGTCGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCTCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATc                                                                                                                                               <  2:163149/150‑1 (MQ=255)
        cTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCa                                                                                                                                              >  2:3306/1‑150 (MQ=255)
             gacgacATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGca                                                                                                                                           <  2:402699/148‑1 (MQ=255)
             gacgacATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGca                                                                                                                                           >  1:402699/1‑148 (MQ=255)
               agacATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATa                                                                                                                                       <  1:162805/149‑1 (MQ=255)
                                    gTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGAt                                                                                                                  <  1:3306/150‑1 (MQ=255)
                                         tttCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGt                                                                                                             >  1:443724/1‑150 (MQ=255)
                                                   caccaGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTAGCGGCTc                                                                                                   >  1:515940/1‑150 (MQ=255)
                                                    accaGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTcc                                                                                                  <  1:734185/150‑1 (MQ=255)
                                                    accaGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTcc                                                                                                  <  1:491559/150‑1 (MQ=255)
                                                      caGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCtt                                                                                                <  2:367803/150‑1 (MQ=255)
                                                        gCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGACCCAGAACAGGCCGAAGTAGATCAACCCCCCACCCCCCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGTTCTTGCGGCTCCTTGt                                                                                              <  2:241253/150‑1 (MQ=255)
                                                           tGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGa                                                                                           >  1:555056/1‑150 (MQ=255)
                                                             atatgctgcACCTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGt                                                                                                             >  1:298031/4‑130 (MQ=255)
                                                             atatgctgcACCTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGt                                                                                                             <  2:298031/127‑1 (MQ=255)
                                                               ctgctgCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTc                                                                                       >  1:113204/1‑150 (MQ=255)
                                                                tgctgcAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTcc                                                                                      >  2:257737/1‑150 (MQ=255)
                                                                tgctgcAGGTGCAGCATATGTGCCGCCCGGCCCGTAGAGATGGCTGATGCC‑ATGGAGATTAACGCCCCACCCCCCAGGGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTcc                                                                                      <  1:775722/150‑1 (MQ=255)
                                                                   tgcAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGcaca                                                                                                                                         <  1:769307/96‑1 (MQ=255)
                                                                   tgcAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGcaca                                                                                                                                         >  2:769307/1‑96 (MQ=255)
                                                                   tgcAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAgg                                                                                                              >  1:180963/1‑123 (MQ=255)
                                                                   tgcAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAgg                                                                                                              <  2:180963/123‑1 (MQ=255)
                                                                        gTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGc                                                                              >  1:727343/1‑150 (MQ=255)
                                                                                  tgtgCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGc                                                                    >  2:492402/1‑150 (MQ=255)
                                                                                    tgCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGa                                                                                                                   >  1:244774/1‑101 (MQ=255)
                                                                                    tgCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGa                                                                                                                   <  2:244774/101‑1 (MQ=255)
                                                                                      ccgccCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCAc                                                                >  2:475175/1‑150 (MQ=255)
                                                                                        gccCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGCCCCAGATCAGCACATAGCCGCGCTGGATGCGCCg                                                                                                                     <  1:101206/95‑1 (MQ=255)
                                                                                        gccCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGCCCCAGATCAGCACATAGCCGCGCTGGATGCGCCg                                                                                                                     >  2:101206/1‑95 (MQ=255)
                                                                                        gccCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGCCCCAGATCAGCACATAGCCGCGCTGGATGCGCCg                                                                                                                     >  2:101187/1‑95 (MQ=255)
                                                                                        gccCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGCCCCAGATCAGCACATAGCCGCGCTGGATGCGCCg                                                                                                                     <  1:101187/95‑1 (MQ=255)
                                                                                                      tCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACa                                                 >  1:765752/1‑150 (MQ=255)
                                                                                                           aaCAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCggg                                            >  1:706998/1‑150 (MQ=255)
                                                                                                            aCAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCGGGa                                           <  2:727343/150‑1 (MQ=255)
                                                                                                                gCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCGGGATGTa                                       <  2:443724/150‑1 (MQ=255)
                                                                                                                        aGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCGGGATGTAGTTCTCGa                               <  2:765752/150‑1 (MQ=255)
                                                                                                                                  cccacccaCCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCGGGATGTAGTTCTCGATGAACAGGTa                     >  1:329570/1‑150 (MQ=255)
                                                                                                                                  cccacccaCCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCGGGATGTAGTTCTCGATGAACAGGTa                     >  1:280992/1‑150 (MQ=255)
                                                                                                                                   ccacccacCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCGGGATGTAGTTCTCGATGAACAGGTAg                    <  1:492402/150‑1 (MQ=255)
                                                                                                                                       ccaccaGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCGGGATGTAGTTCTCGATGAACAGGTAGCgtg                <  1:249738/150‑1 (MQ=255)
                                                                                                                                           caGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCGGGATGTAGTTCTCGATGAACAGGTAGCGTGGTgc            >  1:557702/1‑150 (MQ=255)
                                                                                                                                                    ggCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCGGGATGTAGTTCTCGATGAACAGGTAGCGTGGTGCGCGCTGaaa   <  1:475175/150‑1 (MQ=255)
                                                                                                                                                     gCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTTTCGAACAGCGGGATGTAGTTCTCGATGAACAGGTAGCGTGGTGCGCGCTGAAAc  <  2:706998/150‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                                     
GTGAGCCACTGCCGACGACATTTCACCCAGCGCAACGTAGGTTTCGCTTGCCACCAGCCTGTCCTGCTGCAGGTGCAGCATATGTGCCGCCCGGCGC‑ACGATCCAGAACAGGCCGAAGTAGATCAACGCCCCACCCACCAGTGTCGAGGCCCAGATCAGCACATAGCCGCGCTGGATGCGCCGGATGAGGTCTTGCGGCTCCTTGTAGATTTCCACCATGGCCAGTACCTGCTCACCCTGGCTGTCGAACAGCGGGATGTAGTTCTCGATGAACAGGTAGCGTGGTGCGCGCTGAAAC  >  NC_002947/3871579‑3871876

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑