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_tpiA	2,106,741	0	A	T	96.5%	178.2 / 0.7	57	coding (486/1167 nt)	wbbH	O‑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)                                                gACAATTTGCTTACCAGTATTCAGTATAATTGCAAAGATGAATACGATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTT‑GACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGc                                                                                              >  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)                                                                              tGCAAAGATGAATACGATAAAAACAAGTAAAGTAAATGTTTTACTTACCTTTGTATTAGTAAATTTTTT‑GACCAAATAAATAAAGCAAAAGTAGTTAGAATGATTGGCTGCATGTATGCTGAGAAATTTCTTGATGTGTCTTCAACATc                                                                <  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: ‑