Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_vch_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_vch_tpiA	482,230	0	G	A	98.1%	166.2 / NA	52	P725L (CCG→CTG)	acrB	multidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (28/23);  minor base C (1/0);  total (29/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GACATAAACTTTCTTCACACGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCGGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCTCAAAGTCAAAGCCGGTTGC  >  NC_000913_3_vch_tpiA/482085‑482375                                                                                                                                                  |                                                                                                                                                  gacatAAACTTTCTTCACACGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCaggg                                                                                                                                                <  1:94184/149‑1 (MQ=255)          tttCTTCACACGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCa                                                                                                                                       <  2:393300/149‑1 (MQ=255)              ttcACACGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGAcc                                                                                                                                   >  1:890266/1‑149 (MQ=255)                 acacGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGCCCGtt                                                                                                                                >  1:13346/1‑149 (MQ=255)                 acacCACCTGGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAACCACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGtt                                                                                                                                <  2:159860/149‑1 (MQ=255)                  cacGACCGCGGTCGATAAAGTCGTTCACATAGCTGCAGCCCCATGCAGAAACAAGAGTGGTGTTAATGTAGTTGATAGAAACAACCAGCGCCTGCGATTTTAACAGGTCGGTATCAATCTTAAAATGCCGGGTATCTTCCAGAcagatt                                                                                                                               >  2:30151/1‑144 (MQ=255)                             tCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCt                                                                                                                    >  2:116884/1‑149 (MQ=255)                               gATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTgg                                                                                                                  >  1:817983/1‑149 (MQ=255)                                aTAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGCTTGGACGTACGCTGGt                                                                                                                 >  2:239002/1‑149 (MQ=255)                                 tAAATTCGGTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTc                                                                                                                <  2:81007/149‑1 (MQ=255)                                   aaGCCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCaa                                                                                                              <  2:260109/149‑1 (MQ=255)                                        gTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCagg                                                                                                                                                 <  2:936221/109‑1 (MQ=255)                                         ttCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATTGAAACATCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCGACATATc                                                                                                        >  2:668671/1‑149 (MQ=255)                                         ttCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACatcca                                                                                                        >  2:523066/1‑146 (MQ=255)                                         ttCACATAGCTGCCGCCACATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCGGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACCTACGCGGGTCACCCTATc                                                                                                        >  2:344601/1‑149 (MQ=255)                                            acaTAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTGCAAACCGGTTGGACGTACGCTGGGCAACATATCAgg                                                                                                     >  2:535832/1‑149 (MQ=255)                                            acaTAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAgg                                                                                                     <  2:579814/149‑1 (MQ=255)                                                      cgccCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCgct                                                                                           <  1:116884/149‑1 (MQ=255)                                                        ccccATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCgctgc                                                                                         <  1:373323/149‑1 (MQ=255)                                                        ccccATGCAGCGCCCAGAGTGGTGTTAATGGCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCgctgc                                                                                         <  1:523066/149‑1 (MQ=255)                                                         cccATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCgctgct                                                                                        >  1:141679/1‑149 (MQ=255)                                                          ccATGCAGCGCCTAGAGTGGTGTTAATGTCGTTGATAGAAACTCCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCtt                                                                                       <  2:963040/149‑1 (MQ=255)                                                           cATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGCCCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTc                                                                                      >  2:530189/1‑149 (MQ=255)                                                            attcAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCATCATATCAGGGTGCTTCGCTGCTTCt                                                                                     <  1:946532/146‑1 (MQ=255)                                                                aGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGGCGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTgcaa                                                                                 <  1:646228/149‑1 (MQ=255)                                                                       cgggtggtgTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTg                                                                          <  1:794145/146‑1 (MQ=255)                                                                          gtggtgTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGtt                                                                       >  1:438300/1‑149 (MQ=255)                                                                           tggtgTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTa                                                                      <  2:1019415/149‑1 (MQ=255)                                                                           tggtgTTAAGGTCGTTGACCGCACCACCCAGCGCCTGCGCTGTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCCGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTa                                                                      <  1:344601/149‑1 (MQ=255)                                                                             gtgtTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTAcg                                                                    >  2:591683/1‑149 (MQ=255)                                                                              tgtTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTTTTTTTTTTTTTCAATCTTAAACTGCAGGGTATCTTCCTGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCTCTGCTTCTGCAAGCAACTGAttcccc                                                                   >  2:226036/1‑145 (MQ=255)                                                                                ttAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACgcgc                                                                 >  1:938164/1‑149 (MQ=255)                                                                                        gTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTAGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCa                                                         >  2:918339/1‑149 (MQ=255)                                                                                         ttGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCCACCGGTTACGCGCCTGAGGCAg                                                        >  1:650462/1‑149 (MQ=255)                                                                                            aTAGAAACACCCAGCGCCTGCGCTTTTTTTTTTTTTATCTCACTCTTAAACTGCAGCGTTTGTTCCAGCCCGTTTTGGCGTACGCTCGTCAACATATCAGACTACTTCGCAGCTTCCACAAGCAACTGGTTACGCCCCTGAGTCACttt                                                     >  2:911493/1‑149 (MQ=255)                                                                                              aGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGttttt                                                   <  2:725964/149‑1 (MQ=255)                                                                                               gAAACACCCAGCGCCTGCGCTTTTTCCTGGTGGATATCAATCTTAAATTGTAGGGTATCTTCCAGACCGTTTGGACGTCAGTTGTTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTc                                                  <  1:465576/149‑1 (MQ=255)                                                                                                      ccAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGc                                                                                                 >  1:861178/1‑95 (MQ=255)                                                                                                      ccAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGc                                                                                                 <  2:861178/95‑1 (MQ=255)                                                                                                        aGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAgg                                                                                                     >  2:495004/1‑89 (MQ=255)                                                                                                        aGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAgg                                                                                                     <  1:495004/89‑1 (MQ=255)                                                                                                           gcCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGcc                                      <  2:890266/149‑1 (MQ=255)                                                                                                            ccTGCGCTTTTTCCTGGTCAATATCAATCTAAAACTGCAGAGTATCTACCGGACCGTTTGGACTTACGCTTGTCAACATATCTGTGTGCTTTGCTTCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCa                                     <  2:618085/149‑1 (MQ=255)                                                                                                             cTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAg                                    >  2:916635/1‑149 (MQ=255)                                                                                                              tGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGc                                   <  1:530189/149‑1 (MQ=255)                                                                                                                  cTTTTTCCTGGTCGATATCCATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAAGCCAGCCTgg                               >  1:524822/1‑149 (MQ=255)                                                                                                                   tttttCCTGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGt                              <  2:438300/149‑1 (MQ=255)                                                                                                                          tGGTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAg                       >  1:318805/1‑149 (MQ=255)                                                                                                                            gTCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCt                     >  2:323024/1‑149 (MQ=255)                                                                                                                             tCGATATCAATCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCtc                    >  2:943421/1‑149 (MQ=255)                                                                                                                                     aaTCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCg                                                                                             <  2:687441/68‑1 (MQ=255)                                                                                                                                     aaTCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCg                                                                                             >  1:687441/1‑68 (MQ=255)                                                                                                                                       tCTTAAACTGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCtcaaagtcaaag          >  1:832927/1‑149 (MQ=255)                                                                                                                                               tGCAGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCTCAAAGTCAAAGCCGGTTGc  >  1:595438/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                  GACATAAACTTTCTTCACACGACCGCGGTCGATAAAGTCGTTCACATAGCTGCCGCCCCATGCAGCGCCCAGAGTGGTGTTAATGTCGTTGATAGAAACACCCAGCGCCTGCGCTTTTTCCTGGTCGATATCAATCTTAAACTGCGGGGTATCTTCCAGACCGTTTGGACGTACGCTGGTCAACATATCAGGGTGCTTCGCTGCTTCTGCAAGCAACTGGTTACGCGCCTGAGTCAGTTTTTCGTGACCAAGGCCAGCCTGGTCAATCAGCTCAAAGTCAAAGCCGGTTGC  >  NC_000913_3_vch_tpiA/482085‑482375

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: ‑