Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,969,526 Δ1 bp 8.7% coding (717/2064 nt) fliC ← flagellin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,969,5260G. 8.7% 143.7 / 7.3 46coding (717/2064 nt)fliCflagellin
Reads supporting (aligned to +/- strand):  ref base G (23/19);  new base . (2/2);  total (25/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.97e-01

TGCTGGCATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACTTACCGGCT  >  NC_002947/4969378‑4969667
                                                                                                                                                    |                                                                                                                                             
tGCTGGCATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtg                                                                                                                                               <  1:353094/149‑1 (MQ=255)
tGCTGGCATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtg                                                                                                                                               >  5:381943/1‑149 (MQ=255)
   tGGCATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtg                                                                                                                                            >  5:409018/1‑149 (MQ=255)
     gCATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggt                                                                                                                                          <  6:381943/149‑1 (MQ=255)
      cATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtg                                                                                                                                         <  3:315790/149‑1 (MQ=255)
          gATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtgg                                                                                                                                     <  5:240890/149‑1 (MQ=255)
           aTGGTGAATGCCTGGATGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggt                                                                                                                                    <  2:76243/149‑1 (MQ=255)
            tGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggtg                                                                                                                                   <  6:409018/149‑1 (MQ=255)
                gAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtgg                                                                                                                                     <  6:424091/143‑1 (MQ=255)
                gAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtgg                                                                                                                                     >  5:424091/1‑143 (MQ=255)
                 aaTGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTAc                                                                                                                               <  8:61570/148‑1 (MQ=255)
                      cTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTCTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGt                                                                                                                         >  4:323048/1‑149 (MQ=255)
                          gTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAg                                                                                                                     >  3:278902/1‑149 (MQ=255)
                                tCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCaa                                                                                                               <  2:303044/149‑1 (MQ=255)
                                tCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTACAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTAACCAAGTTCAGCACGaa                                                                                                               >  5:392021/1‑149 (MQ=255)
                                        cAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTAcc                                                                                                         <  4:106336/147‑1 (MQ=255)
                                           tGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcag                                                                                                    >  3:98403/1‑149 (MQ=255)
                                              aCCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTACAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcagcag                                                                                                 >  1:15925/1‑149 (MQ=255)
                                                cAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCGGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcagcagca                                                                                               >  8:77466/1‑149 (MQ=255)
                                                cAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTCTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcagcagca                                                                                               >  1:266673/1‑149 (MQ=255)
                                                  gTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCAcc                                                                                             >  7:86446/1‑149 (MQ=255)
                                                   tGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcagcag                                                                                                 <  7:212263/144‑1 (MQ=255)
                                                   tGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcagcag                                                                                                 >  8:212263/1‑144 (MQ=255)
                                                     gcgcTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGAt                                                                                          <  8:86446/149‑1 (MQ=255)
                                                        cTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAACTTACAGCCAGCAGCACCGATGGt                                                                                       >  7:192196/1‑149 (MQ=255)
                                                               tGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGA‑‑‑TGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCgg                                                                                    >  6:47670/1‑142 (MQ=255)
                                                               tGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGA‑‑‑TGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCgg                                                                                    <  5:47670/142‑1 (MQ=255)
                                                               tGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGA‑‑‑TGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCgg                                                                                    <  3:231409/142‑1 (MQ=255)
                                                               tGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGA‑‑‑TGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCgg                                                                                    >  4:231409/1‑142 (MQ=255)
                                                                 cTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTAt                                                                               >  6:302963/1‑148 (MQ=255)
                                                                 cTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATc                                                                              <  4:278902/149‑1 (MQ=255)
                                                                 cTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATc                                                                              <  4:98403/149‑1 (MQ=255)
                                                                 cTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTACAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTAt                                                                               <  2:15925/148‑1 (MQ=255)
                                                                  tAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATc                                                                              >  5:415978/1‑148 (MQ=255)
                                                                    gctgTAACACCTGTATTTATAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCTATGTTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCaaa                                                                           <  6:392021/146‑1 (MQ=255)
                                                                    gCGGTAACACCTGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATc                                                                              <  3:323048/146‑1 (MQ=255)
                                                                                   ttGCTAGTCTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTg                                                             <  2:266673/148‑1 (MQ=255)
                                                                                           ttCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCca                                                    >  1:373438/1‑149 (MQ=255)
                                                                                            atgtggTTGACAATATCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCca                                                    >  7:325964/5‑148 (MQ=255)
                                                                                                ggTTGATATTGTCCACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAAcc                                               <  5:302963/149‑1 (MQ=255)
                                                                                                ggTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggtgg                                                                                                                                  <  3:192897/66‑1 (MQ=255)
                                                                                                ggTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggtgg                                                                                                                                  >  4:192897/1‑66 (MQ=255)
                                                                                                 gTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAAcc                                               >  3:70576/1‑148 (MQ=255)
                                                                                                         tGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACaa                                                 >  2:275576/1‑138 (MQ=255)
                                                                                                         tGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACaa                                                 <  1:275576/138‑1 (MQ=255)
                                                                                                              aCCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGtgct                                 >  3:364883/1‑149 (MQ=255)
                                                                                                                cacaTCCTGCAGGGTGTCGCCTGCCGCGGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGtgctgc                               <  7:77466/149‑1 (MQ=255)
                                                                                                                                tCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGcc               >  4:35377/1‑149 (MQ=255)
                                                                                                                                  gCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCa                             <  4:183467/133‑1 (MQ=255)
                                                                                                                                  gCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCa                             >  3:183467/1‑133 (MQ=255)
                                                                                                                                     tGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCAttgt                      >  2:267480/1‑137 (MQ=255)
                                                                                                                                     tGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCAttgt                      <  1:267480/137‑1 (MQ=255)
                                                                                                                                        cGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCAtt                        <  6:417532/132‑1 (MQ=255)
                                                                                                                                        cGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCAtt                        >  5:417532/1‑132 (MQ=255)
                                                                                                                                          cagcagCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACTTACCg     >  3:186872/1‑149 (MQ=255)
                                                                                                                                             cagcGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACt          <  2:233357/141‑1 (MQ=255)
                                                                                                                                             cagcGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACt          >  1:233357/1‑141 (MQ=255)
                                                                                                                                             cagcGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACTTACCGGCt  <  4:70576/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                             
TGCTGGCATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACTTACCGGCT  >  NC_002947/4969378‑4969667

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: ‑