Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,426,632 G→A 13.2% P88S (CCG→TCG)  PP_2127 ← sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,426,6320GA13.2% 107.5 / 7.2 46P88S (CCG→TCG) PP_2127sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (16/23);  new base A (3/3);  total (19/27)
Fisher's exact test for biased strand distribution p-value = 6.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

CTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGCCACGCACAGCC  >  NC_002947/2426489‑2426778
                                                                                                                                                |                                                                                                                                                  
cTCGTCGGGCCAGTGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTCCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCGCCTTGAGCATGCGCCCGGCCGAGCT‑GGCCGAGCGCa                                                                                                                                               <  1:329127/149‑1 (MQ=255)
   gtcgGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAgg                                                                                                                                             <  4:43212/148‑1 (MQ=255)
   gtcgGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGt                                                                                                                                            <  5:251918/149‑1 (MQ=255)
   gtcgGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCCCGGCCGAGCT‑GGCCGAGCGCat                                                                                                                                              <  7:273296/147‑2 (MQ=255)
   gtcgGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCCCGGCCGAGCT‑GGCCGAGCGCat                                                                                                                                              <  4:44143/147‑2 (MQ=255)
                       gCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTTGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCgcccagg                                                                                                                        <  1:88468/149‑1 (MQ=255)
                         cACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCgcccaggcc                                                                                                                      >  4:18911/1‑149 (MQ=255)
                               aGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTg                                                                                                                <  7:213885/149‑1 (MQ=255)
                               aGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTg                                                                                                                <  4:341592/149‑1 (MQ=255)
                                 ttGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTa                                                                                                              <  2:13474/149‑1 (MQ=255)
                                 ttGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTa                                                                                                              <  3:18911/149‑1 (MQ=255)
                                     aGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTacaac                                                                                                          <  6:211483/149‑1 (MQ=255)
                                     aGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTacaa                                                                                                           >  8:355209/1‑148 (MQ=255)
                                     aGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTacaa                                                                                                           >  2:69135/1‑148 (MQ=255)
                                      gCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTTCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGAGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTTTacaaca                                                                                                         <  8:322106/149‑1 (MQ=255)
                                      gCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTacaa                                                                                                           >  6:351525/1‑147 (MQ=255)
                                                    aGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTgg                                                                                            <  7:286727/148‑1 (MQ=255)
                                                         ttGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGGC‑AGCTCGCCCGGGCGCACGTGGAACGACCTGGCGCCCCGGCCCAGTTGTACAACAGCACCCACCGTGGCGAcc                                                                                       >  2:229472/1‑148 (MQ=255)
                                                           gACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCaa                                                                                     <  2:223509/148‑1 (MQ=255)
                                                             ccGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTg                                                                                  <  5:351525/149‑1 (MQ=255)
                                                                    cgtcgtGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTTCAACAGCACCCAGCGAGGCGACGAACTGCAGCAcc                                                                           >  7:184392/1‑149 (MQ=255)
                                                                      tcgtGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACcag                                                                         >  1:6864/1‑149 (MQ=255)
                                                                        gtGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACcagca                                                                       <  7:355209/149‑1 (MQ=255)
                                                                         tGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACcagcag                                                                      >  1:87908/1‑149 (MQ=255)
                                                                          gCAGTTACCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAgg                                                                     >  2:339055/1‑149 (MQ=255)
                                                                                cccGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGcc                                                               >  6:253076/1‑149 (MQ=255)
                                                                                   ggCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCggg                                                            <  2:87908/149‑1 (MQ=255)
                                                                                        aGATGCTGGCGCTCGTCTTCTTGCAACTTGAGCCTGCGCTCGTCC‑ATCTCGGCCGTGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCTTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGc                                                       <  5:44003/149‑1 (MQ=255)
                                                                                           tGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTg                                                    <  6:210490/149‑1 (MQ=255)
                                                                                             cTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGt                                                  <  1:234874/149‑1 (MQ=255)
                                                                                             cTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGt                                                  >  2:234874/1‑149 (MQ=255)
                                                                                             cTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGACC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTgg                                                   <  7:152288/148‑1 (MQ=255)
                                                                                                gcgcTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGtt                                                 <  6:222540/147‑1 (MQ=255)
                                                                                                        cttcttGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTa                                        >  3:333705/1‑148 (MQ=255)
                                                                                                                  cTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGt                             <  5:253076/149‑1 (MQ=255)
                                                                                                                     gAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTg                           <  2:353060/148‑1 (MQ=255)
                                                                                                                        cATGCGCTCGGCC‑AGCTCGTCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCCACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGtt                            >  6:64147/1‑144 (MQ=255)
                                                                                                                        cATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGtt                            <  5:64147/144‑1 (MQ=255)
                                                                                                                         ctGCGCCCGGCCGAGCT‑GGCCGAGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAAt                      >  8:123901/2‑149 (MQ=255)
                                                                                                                           gcgcCCGGCCGAGCT‑GGCCGAGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTTGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAAt                      >  2:241445/1‑147 (MQ=255)
                                                                                                                           gcgcCCGGCCGAGCT‑GGACGAGCGCAGGTGGATCGACCTGGCGAACAGGCCCAGTTGTACAACATCACACAGCGTGGAGACCAACTGCAGCACCAGCAGGCTGGACGGGATTGCCTGGTTGTCCAGGTACAGCGCCATGTTGGCAAt                      >  2:246804/1‑147 (MQ=255)
                                                                                                                             gcTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGt                  >  6:97504/1‑149 (MQ=255)
                                                                                                                                 cgCC‑AGCTCGGCCGGGCGCAGATGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAgg              <  2:167440/148‑1 (MQ=255)
                                                                                                                                  gCC‑AGCTCGGCCGGGCGCAGGTGGATCAACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGc             >  8:147502/1‑149 (MQ=255)
                                                                                                                                    c‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGCCa           >  2:136419/1‑149 (MQ=255)
                                                                                                                                              cGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGCCACGCACAGcc  <  4:363077/149‑1 (MQ=255)
                                                                                                                                                ggCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGCCACGc        <  6:361106/141‑1 (MQ=255)
                                                                                                                                                ggCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGCCACGc        >  5:361106/1‑141 (MQ=255)
                                                                                                                                                |                                                                                                                                                  
CTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGCCACGCACAGCC  >  NC_002947/2426489‑2426778

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑