Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,963,934	G→A	P373S (CCG→TCG)	flhA ←	flagellar biosynthesis protein FlhA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,963,934	0	G	A	100.0%	228.0 / NA	63	P373S (CCG→TCG)	flhA	flagellar biosynthesis protein FlhA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (31/32);  total (31/32)

TAGCGGGCAGGTTGCAGATCCATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGGGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCC  >  NC_000913/1963798‑1964066                                                                                                                                         |                                                                                                                                     tAGCGGGCAGGTTGCAGATCCATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGAt                                                                                                                                   <  2:1025780/140‑1 (MQ=255)      ggCAGGTTGCAGATCCATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTc                                                                                                                              >  1:627857/1‑140 (MQ=255)        cAGGTTGCAGATCCATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGa                                                                                                                            <  2:864020/140‑1 (MQ=255)        cAGGTTGCAGATCCATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGa                                                                                                                            <  1:1112720/140‑1 (MQ=255)        cAGGTTGCAGATCCATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGa                                                                                                                            <  1:451251/140‑1 (MQ=255)         aGGTTGCAGATCCATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGAt                                                                                                                           <  1:986135/140‑1 (MQ=255)             tGCAGATCCATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAAcc                                                                                                                       >  2:971692/1‑140 (MQ=255)               cAGATCCATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCa                                                                                                                     <  1:99073/140‑1 (MQ=255)                   tCCATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTc                                                                                                                 <  1:337075/140‑1 (MQ=255)                     cATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCa                                                                                                               >  2:652933/1‑140 (MQ=255)                       tatTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCAtt                                                                                                             >  2:388883/1‑140 (MQ=255)                       tatTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCAtt                                                                                                             >  2:594287/1‑140 (MQ=255)                            tCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCag                                                                                                        >  1:993407/1‑140 (MQ=255)                              gcgAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCagag                                                                                                      >  2:357606/1‑140 (MQ=255)                              gcgAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCagag                                                                                                      >  1:909209/1‑140 (MQ=255)                                gAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGaa                                                                                                    >  2:1036954/1‑140 (MQ=255)                                 aaTGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAAt                                                                                                   >  1:1139179/1‑140 (MQ=255)                                   tgtgCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCt                                                                                                 >  2:217039/1‑140 (MQ=255)                                   tgtgCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCt                                                                                                 <  2:939818/140‑1 (MQ=255)                                     tgCACCACTGGCGGCAGAAATCCCATCTCCTGGGCTAATTTCTTGCGTATACTGCGTATACGGCCCAACAATTCACCATCCTTCTGAAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTc                                                                                               <  2:236414/140‑1 (MQ=255)                                     tgCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTc                                                                                               <  2:1139179/140‑1 (MQ=255)                                     tgCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTc                                                                                               <  1:1013469/140‑1 (MQ=255)                                      gCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTcc                                                                                              >  2:112978/1‑140 (MQ=255)                                      gCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTcc                                                                                              <  1:984233/140‑1 (MQ=255)                                            cTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGt                                                                                        >  1:31298/1‑140 (MQ=255)                                             tGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTa                                                                                       <  1:594287/140‑1 (MQ=255)                                             tGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTa                                                                                       <  1:849980/140‑1 (MQ=255)                                              ggcggcAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTAc                                                                                      <  1:652933/140‑1 (MQ=255)                                                cggcAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACAt                                                                                    >  1:1013167/1‑140 (MQ=255)                                                          cccATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGt                                                                          <  2:553979/140‑1 (MQ=255)                                                                tcCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTc                                                                    >  1:487476/1‑140 (MQ=255)                                                                tcCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTc                                                                    <  1:388883/140‑1 (MQ=255)                                                                  cTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGa                                                                  <  2:45252/140‑1 (MQ=255)                                                                  cTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGa                                                                  >  1:327455/1‑140 (MQ=255)                                                                   tGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGAc                                                                 <  1:217039/140‑1 (MQ=255)                                                                     ggCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACaa                                                               <  1:112978/140‑1 (MQ=255)                                                                     ggCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACaa                                                               <  2:585342/140‑1 (MQ=255)                                                                     ggCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACaa                                                               >  1:1039835/1‑140 (MQ=255)                                                                     ggCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACaa                                                               <  1:1036954/140‑1 (MQ=255)                                                                     ggCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACaa                                                               >  2:160806/1‑140 (MQ=255)                                                                       cAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACg                                                             <  1:337731/140‑1 (MQ=255)                                                                          aTTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGta                                                          <  1:971692/140‑1 (MQ=255)                                                                                    gATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTg                                                >  2:301825/1‑140 (MQ=255)                                                                                           cGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCAtttt                                         >  2:717858/1‑140 (MQ=255)                                                                                             tataCGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTa                                       <  2:487476/140‑1 (MQ=255)                                                                                              ataCGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTAc                                      <  2:1039835/140‑1 (MQ=255)                                                                                               taCGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTAcc                                     >  2:550050/1‑140 (MQ=255)                                                                                                aCGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCg                                    >  1:839907/1‑140 (MQ=255)                                                                                                   gCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGtt                                 >  2:926468/1‑140 (MQ=255)                                                                                                   gCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGtt                                 >  1:1012196/1‑140 (MQ=255)                                                                                                   gCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGtt                                 >  1:178147/1‑140 (MQ=255)                                                                                                   gCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGtt                                 >  2:757737/1‑140 (MQ=255)                                                                                                         caacTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTCCCATTTTTACCGGTTTGGGtt                           <  2:909209/140‑1 (MQ=255)                                                                                                            cTCACCATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCgg                        >  2:559010/1‑140 (MQ=255)                                                                                                                ccATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAgg                    <  2:993407/140‑1 (MQ=255)                                                                                                                 cATCCTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGgc                   >  2:484055/1‑140 (MQ=255)                                                                                                                    ccTGCTGGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCt                <  2:327455/140‑1 (MQ=255)                                                                                                                         tgGAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTg           >  2:151447/1‑140 (MQ=255)                                                                                                                           gAAATCGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGtt         >  1:439291/1‑140 (MQ=255)                                                                                                                                cGACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGt    <  1:484055/140‑1 (MQ=255)                                                                                                                                 gACCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCGCGTCGCTTCGACATCGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTc   <  2:1012196/140‑1 (MQ=255)                                                                                                                                  aCCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTcc  <  2:627857/140‑1 (MQ=255)                                                                                                                                  aCCATCGAGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTcc  >  2:921201/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                     TAGCGGGCAGGTTGCAGATCCATATTGTCGCGAATGTGCACCACTGGCGGCAGAAATCCCATCTCCTGGGCAAATTTCTTGCGGATACTGCGTATACGGCCCAACAACTCACCATCCTGCTGGAAATCGACCATCGGGATCAGTCGATAACCCACTTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCC  >  NC_000913/1963798‑1964066

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑