Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_vch_tpiA 2,106,741 A→T S162S (TCT→TCA wbbH ← O‑antigen polymerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_vch_tpiA2,106,7410AT96.5% 178.2 / 0.7 57coding (486/1167 nt)wbbHO‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (30/25);  minor base . (1/1);  total (31/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.50e-01

ACTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACC  >  NC_000913_3_vch_tpiA/2106595‑2106883
                                                                                                                                                  |                                                                                                                                              
aCTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGa                                                                                                                                              <  1:593537/149‑1 (MQ=255)
 ctctATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGAc                                                                                                                                             >  1:320710/1‑149 (MQ=255)
      ttAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCaaat                                                                                                                                        >  2:204290/1‑149 (MQ=255)
             cTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAttatataag                                                                                                                                 >  2:778900/1‑148 (MQ=255)
             cTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAAtaaataaa                                                                                                                                 <  1:204290/149‑1 (MQ=255)
              tACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTTTTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAg                                                                                                                                <  1:61715/149‑1 (MQ=255)
                   tGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCaaaa                                                                                                                           <  1:561735/149‑1 (MQ=255)
                   tGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTCTATTAGTAAATTTTTTTGCCCCAATAAATAAAGCaaat                                                                                                                           >  2:397657/1‑148 (MQ=255)
                          aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTa                                                                                                                    >  2:243676/1‑149 (MQ=255)
                          aTAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTa                                                                                                                    >  1:223173/1‑149 (MQ=255)
                          aTAAGAGATGATAACCATAAAGAAAATTTGATTACCATTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACAAAATAAATAAAGCAAAAGTAGTTa                                                                                                                    <  2:253639/149‑1 (MQ=255)
                           tAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTCGTTAg                                                                                                                   >  2:377642/1‑149 (MQ=255)
                           tAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAg                                                                                                                   >  1:330155/1‑149 (MQ=255)
                            aaGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTAAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAGGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAACGTAAAAGTATTTAGa                                                                                                                  >  2:202174/1‑149 (MQ=255)
                              gagaTTATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTTCATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAt                                                                                                                <  1:775460/149‑1 (MQ=255)
                                 atgatAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTACCTATTAAATAAAGCAAAAGTAGTTAGAATGAt                                                                                                             >  2:470828/1‑149 (MQ=255)
                                 atgatAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGAt                                                                                                             >  2:495806/1‑149 (MQ=255)
                                 atgatAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTACTAATCAATTTTGTTTACCAAATAAATAAAGCACAAGTAGATAGAAAGAt                                                                                                             >  1:343540/1‑149 (MQ=255)
                                    atAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTgg                                                                                                          <  2:226338/149‑1 (MQ=255)
                                               gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACGATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGc                                                                                              >  2:585169/1‑149 (MQ=255)
                                                   aTTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTga                                                                                           >  1:475936/1‑149 (MQ=255)
                                                   aTTTGCCTACAAGTATGCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTga                                                                                           <  1:298268/149‑1 (MQ=255)
                                                         ttACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTGGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAATAGTTAGAATGTTGGGCGGCATGTATGCTGTGAACtt                                                                                     >  1:371431/1‑149 (MQ=255)
                                                               gTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGa                                                                               <  1:280366/149‑1 (MQ=255)
                                                               gTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAAGGATGGGCTGCATGTATGCTGAGAAATTTCTTGa                                                                               >  1:733531/1‑149 (MQ=255)
                                                                   tCAGTATCATTGCAAAAATAAATACAATAAAAACAAGTAAAGCAGATGGTTTACTTACCTTTGTATAAGTAGCTTTTTTTGACCAAATACATAAAGCAAAAGTACTTAGAATGAATAGCTGCATATATACTGAGAAAATTCTTGAtttg                                                                           >  2:239670/1‑149 (MQ=255)
                                                                        ataAGTGCAAATATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTc                                                                      <  1:14273/149‑1 (MQ=255)
                                                                            ttGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                            >  2:652144/1‑139 (MQ=255)
                                                                            ttGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGAtgt                                                                            <  1:652144/139‑1 (MQ=255)
                                                                             tGCAAAGATGAATACGATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATc                                                                <  1:585169/149‑1 (MQ=255)
                                                                               cAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTCCTTACCTTTGTATTAGTAAATTTTTTTTTTTAATTTTTTAAAGCAACAGTAGGTAGAATGATTGGCTGCTGGTTTCCGGATAGAATTCTTGTTTCTTCTACAACATCa                                                               >  2:329427/1‑149 (MQ=255)
                                                                                aaaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAg                                                              >  2:335789/1‑149 (MQ=255)
                                                                                 aaGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGc                                                             <  1:335789/149‑1 (MQ=255)
                                                                                         tACAATAAAAACAAGCTAAGTAAATGTTTTAACTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTACGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTa                                                     <  2:140279/149‑1 (MQ=255)
                                                                                               aaaaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAAt                                               <  2:141387/149‑1 (MQ=255)
                                                                                                aaaaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAAtt                                              <  2:322424/149‑1 (MQ=255)
                                                                                                  aaCAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCa                                            <  1:407435/149‑1 (MQ=255)
                                                                                                    cAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCata                                          <  2:600621/149‑1 (MQ=255)
                                                                                                     aagtaaagtaAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCACATTCatat                                         >  1:249516/1‑149 (MQ=255)
                                                                                                       gtaaagtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAg                                       <  1:21886/149‑1 (MQ=255)
                                                                                                           agtaaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaa                                   >  1:277906/1‑149 (MQ=255)
                                                                                                             taaaTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTTACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagt                                 >  1:151289/1‑149 (MQ=255)
                                                                                                              gaaTGTTTTACTTGGCTTTGTAGTAGTGAATTTTTTTGACCAGTTTATTGTAGCGAAGGTGGTTAGGATGGTTGGCTGCATGTATGCTGAGAAATTTCTGGATGTGTCGTCAACATCATTGTCTCTTGTCAAATTTATATAGTtaggtg                                >  2:398560/2‑148 (MQ=255)
                                                                                                                aTGTTTTACTTACCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCtaagtaag                              <  1:492736/149‑1 (MQ=255)
                                                                                                                         ttacCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGAAAAAGTAGATAGAATGATTGGATGCATGTCTGCTGAGAAATTTCTTGATATGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCg                     >  1:193933/1‑149 (MQ=255)
                                                                                                                           acCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGTTAGTCCCGaa                   <  1:763852/149‑1 (MQ=255)
                                                                                                                           acCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGaa                   <  1:763866/149‑1 (MQ=255)
                                                                                                                           acCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGaa                   >  2:763852/1‑149 (MQ=255)
                                                                                                                           acCTTTGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGaa                   >  2:763866/1‑149 (MQ=255)
                                                                                                                              tttGTATTAGTAAATTTTTTTGACCAAATAACTAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg                <  2:15671/149‑1 (MQ=255)
                                                                                                                              tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg                <  1:732026/149‑1 (MQ=255)
                                                                                                                              tttGTATTAGTAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTg                <  1:243676/149‑1 (MQ=255)
                                                                                                                                        tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACtt      >  1:629115/1‑149 (MQ=255)
                                                                                                                                        tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACtt      >  2:91067/1‑149 (MQ=255)
                                                                                                                                        tAAATTTTTTTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTATTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCTCAAACTGGTAGTTACtt      >  2:585124/1‑149 (MQ=255)
                                                                                                                                          aaTTTTTTTGACCAAATAAATAAAGGAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTaa    <  2:693108/149‑1 (MQ=255)
                                                                                                                                            ttttttTGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAAcc  >  1:556835/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                              
ACTCTATTAACACCTACGATGAATGCATAAGAGATGATAACCATAAAGACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACAATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTTAGACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATCAGCATCTCTTATCAAATTCATATAGCTAAGTAAGCTAGTCCCGAACTGGTAGTTACTTAACC  >  NC_000913_3_vch_tpiA/2106595‑2106883

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: