Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	482,230	G→A	P725L (CCG→CTG)	acrB ←	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	482,230	0	G	A	96.1%	157.3 / ‑5.3	51	P725L (CCG→CTG)	acrB	multidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (28/21);  minor base C (1/1);  total (29/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

TGACATAAACTTTCTTCACACGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCGGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCTCAAAGTCAAAGCCGGTTG  >  NC_000913_3_pae_tpiA/482084‑482374                                                                                                                                                    |                                                                                                                                                 tgacatAAACTTTCTTCACACGACCGCGGTCGATAAAGTCGTTCACAAAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCagg                                                                                                                                                >  1:291535/1‑149 (MQ=255)    catAAACTTTCTTCACCCGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCGGCGCCCAGAGTGGTGTTAATG‑CCGTTGATACAAACACCCAGCGCCTGCGCTTTTTCCTCGTCCATATCAACCTTAAGCTGCAGGGTa                                                                                                                                             >  2:358161/1‑149 (MQ=255)      tAAACGGTCTGCACACGACCGCGGTCGTTAAAGTCGTTCACATGGCTGCCGCCCCATGCAGCGCCCAGTGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATc                                                                                                                                           <  2:302526/149‑1 (MQ=255)        aaCTTTCTTCACACGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCtt                                                                                                                                         >  1:524668/1‑149 (MQ=255)         aggtccttcGCACGACTGCGGTCGATAAAGTCGTGCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTCGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTc                                                                                                                                        <  2:623055/144‑1 (MQ=255)                tcACACGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCGCCATGCAGGGCCAGGCAGAGTG‑GAATGCAAGTAGATCGGAAGCGCTAGCGCCAGCTCTTTTGCCGGGGCGGAACCAATCTTAAACTGCCGGGGAGCTTCCAGAcga                                                                                                                                 >  1:164035/1‑147 (MQ=255)                  acacGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATAACAATCTTAAACTGCAGGGTATCTTCCAGACCGtt                                                                                                                               >  2:264941/1‑149 (MQ=255)                  acacGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGACCGGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGAGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGCTACCTTCAAGACCggt                                                                                                                               >  2:314153/1‑147 (MQ=255)                   cacGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCGTAAACTGCAGGGTATCTTCCAGACCGttt                                                                                                                              <  1:342962/149‑1 (MQ=255)                    acGTCCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTg                                                                                                                             <  1:540426/149‑1 (MQ=255)                       aCCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCCGGGTATCTTGCAGACCGTTTGGAc                                                                                                                          <  1:599294/149‑1 (MQ=255)                             gtggATAATGTCGTTCACAGTGCTGCTGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGATCGTTTGGACGTACGc                                                                                                                    <  2:422868/146‑1 (MQ=255)                               cGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTg                                                                                                                  <  2:481418/149‑1 (MQ=255)                               cGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTg                                                                                                                  <  2:540147/149‑1 (MQ=255)                                     aGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAAc                                                                                                            <  2:168843/149‑1 (MQ=255)                                     aGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAAc                                                                                                            >  1:168843/1‑149 (MQ=255)                                             acaTAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACGCCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAgg                                                                                                    >  1:654163/1‑149 (MQ=255)                                             acaTAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAgg                                                                                                    <  2:195621/149‑1 (MQ=255)                                                    tGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTc                                                                                             >  1:219107/1‑149 (MQ=255)                                                        gccCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATACCAGGGTGCTTCgctg                                                                                         >  2:530930/1‑149 (MQ=255)                                                             aTGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCt                                                                                    >  1:459921/1‑149 (MQ=255)                                                                      ccAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACACTGGTCACGATATCTGGGTGCTTCGCTGATTCTACAAGCAAc                                                                           >  2:10978/1‑149 (MQ=255)                                                                          agTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGt                                                                       <  2:403152/149‑1 (MQ=255)                                                                                   aaTG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCATTCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACccgcgt                                                              >  1:59067/1‑147 (MQ=255)                                                                                     tG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGttt                                                                                                                              <  2:230354/83‑1 (MQ=255)                                                                                     tG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGttt                                                                                                                              >  1:230354/1‑83 (MQ=255)                                                                                        tCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGt                                                          <  2:653049/149‑1 (MQ=255)                                                                                        gcgtggttAGAAACTCCCAGCGCCTCCACTGTTTCCTGGTCGATATCAATCTTAAACGGCAGGGTATCTTCCAGACCGTTTGGACGAACGCTGGTAAGCATATCAGGGTGCTACGCTGCTTCTGCAAGCTACTGGTTACGAGCCTGAGt                                                          <  2:686508/142‑1 (MQ=255)                                                                                          gTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCa                                                        <  2:654168/149‑1 (MQ=255)                                                                                           ttGATAGAAACACCCAGCGCCTGCGCTTTTTTTTTTTTTTTTTTAATCTTAAACCGCAGGGTATCTTGCAGACCGTTTGAACGGAGGCTGGTCAGCAGATCAGGTTGCTTCGCTGCTTATGCACGCAACTGGTCCCGCGCCTCAGTccg                                                       >  2:166092/1‑147 (MQ=255)                                                                                           ttGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAg                                                       >  2:30274/1‑149 (MQ=255)                                                                                             gATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGtt                                                     <  1:406718/149‑1 (MQ=255)                                                                                             gATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCCCCTGAGTCACtt                                                     >  1:176268/1‑149 (MQ=255)                                                                                              aTAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGttt                                                    >  1:48560/1‑149 (MQ=255)                                                                                               tAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGAGTGCTTCGCTGCTTCTGCAAGCACCTGGTTACGAGCCTGAGTCGGtttt                                                   >  2:15963/1‑149 (MQ=255)                                                                                                   aaCACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCGTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGt                                               <  2:558228/149‑1 (MQ=255)                                                                                                    acacCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCtt                                                                                      >  2:16359/1‑109 (MQ=255)                                                                                                    acacCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCtt                                                                                      <  1:16359/109‑1 (MQ=255)                                                                                                      acCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGAc                                            >  1:501155/1‑149 (MQ=255)                                                                                                           gcgcCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCACgg                                       >  1:325750/1‑149 (MQ=255)                                                                                                                     tttttCCTGGTTGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGt                             <  1:500646/149‑1 (MQ=255)                                                                                                                     tttttCCTGGTCGATATCAATCTTAAACTGAAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTgtt                             >  2:445986/1‑147 (MQ=255)                                                                                                                          ccTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTAGGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCCGGTCAATc                        >  2:691805/1‑149 (MQ=255)                                                                                                                            tGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCATAAGTCAGTTTTTCGTGACCAAAGCCAGCCTGGTCAATCAg                      >  1:477712/1‑149 (MQ=255)                                                                                                                             ggTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGc                     >  1:38686/1‑149 (MQ=255)                                                                                                                                       aaTCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAAGCCAGCCTGGTCAATCAGCcaaaagtcaa           >  2:129309/1‑149 (MQ=255)                                                                                                                                        ggcTTAAACGGTAGGGTATTTTTCGGACCGTTTGGACGTACGCTGGTGATGATTTCAGGGTGCTTGGCTGCTGCTGCAAGCGACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGGCTGGTCAATCAGCtcaagggcaaa          <  2:528238/147‑1 (MQ=255)                                                                                                                                         tCTTAAACTGCAGGGTATCTTCCAGACCGTATGGACGTACGCTGATCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCACCTGGTTACGCGCCTGAATCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCtccagatcaaat         >  2:271333/1‑148 (MQ=255)                                                                                                                                               aCTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGa                                             >  2:542725/1‑107 (MQ=255)                                                                                                                                               aCTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACAGATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGa                                             <  1:542725/107‑1 (MQ=255)                                                                                                                                                 tGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCTCAAAGTCAAAGCCGGTTg  <  1:95785/148‑1 (MQ=255)                                                                                                                                                 tGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCTCAAAGTCAAAGCCGGTTg  >  2:95785/1‑148 (MQ=255)                                                                                                                                                    |                                                                                                                                                 TGACATAAACTTTCTTCACACGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATG‑TCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCGGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCTCAAAGTCAAAGCCGGTTG  >  NC_000913_3_pae_tpiA/482084‑482374

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑