Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	883,396	C→T	intergenic (‑8/‑277)	ybjG ← / → mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	883,396	0	C	T	97.0%	105.0 / NA	33	intergenic (‑8/‑277)	ybjG/mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (11/21);  minor base A (1/0);  total (12/21)
Fisher's exact test for biased strand distribution p-value = 3.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GAAAAAGATGTCCCATCGTCCAGGACACAAACAGGCTGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCCGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCG  >  NC_000913/883154‑883620                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                 gAAAAAGATGTCCCATCGTCCAGGACACAAACAGGCAGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCaaa                                                                                                                                                                                                                          <  1:500494/251‑1 (MQ=255)                         acacAAACAGGCTGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAg                                                                                                                                                                                                  <  2:320116/251‑1 (MQ=255)                          aacaAACTGGCTGACCGCCAGCGCGATAGCGAGTTCGATCACCAGTTGCCGTTGTGCTGTAAGCCCTACCAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAAAAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGAGTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGAGTAAAAGGGAGCCAATACAgg                                                                                                                                                                                                 <  2:128848/250‑1 (MQ=255)                             aaaCAGGCTGACCGCCAGCGCGAGAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCTCCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCaa                                                                                                                                                                                              <  1:90041/251‑1 (MQ=255)                              aaCAGGCTGCCCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAAGTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAg                                                                                                                                                                                             <  2:162181/251‑1 (MQ=255)                                       aCCGCCAGCGCTATAGCGATTTTTAACACCAGTTGCCGTTGTGCTTTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGGAATCAAATCTTTATCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACTCAAAGTGAGTAAAAGGGAGCCAATACAGGCAAGTCGTTgag                                                                                                                                                                                     <  2:653909/250‑1 (MQ=255)                                          gCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAAt                                                                                                                                                                                  >  1:132679/1‑250 (MQ=255)                                          gCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAAt                                                                                                                                                                                  >  2:349875/1‑250 (MQ=255)                                            cAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGAGTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGCCGTTGAGAATaaa                                                                                                                                                                               <  1:549939/251‑1 (MQ=255)                                                     aGCGATTTTTATTACCAGGTGTCGTTGTGCGTTAAGCCCCCACAAACAAAGCACCACGGCCAGCAACGGCACCACGGTAAGCAAATCTTTAGCAATAAAAAACGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGATAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATCCAGGCAAGTCGTTGAGAATAAAGTGCAGGtt                                                                                                                                                                      <  2:517725/251‑1 (MQ=255)                                                     aGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGt                                                                                                                                                                       <  1:349875/250‑1 (MQ=255)                                                      gCGATTGTTACCACCAGGTGCCGTTTTGCTGTAAGCCCCTACAACCAAAGTCCCACGGTCAGCAACGGAACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCGACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCATAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGtt                                                                                                                                                                      <  2:673540/250‑1 (MQ=255)                                                          tttttATCACCAGTTGCCGTTGTGATGTAAGCCCCCACAACCACAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGACGTCGCGTTAATAAGCGAGAATAGAGAGAGATTCAAATTTTCCAGCATACCTTCCAGACGCAACGTGATTAAAAGGGAGCCAATCAAGGCAAGTCGTTGAGTATAAAGTGAAGATTAAACt                                                                                                                                                                 >  2:611757/1‑251 (MQ=255)                                                           ttttATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACt                                                                                                                                                                 <  1:359449/250‑1 (MQ=255)                                                               ataaCCAGTGGCCGTGGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAACAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGAACATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGt                                                                                                                                                             <  2:505258/247‑1 (MQ=255)                                                                 cACCAGTTGCCGTTGTGCTGTAAGCCCCCACACCCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCACCGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGCGAGAATAGAGAGAGATTCAACTTTTCCAGCATCACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGACGTTGAGAATAACGTGCAGGTTAAAATGGGTaa                                                                                                                                                           >  2:258662/1‑250 (MQ=255)                                                                 cACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTaa                                                                                                                                                           <  1:484321/250‑1 (MQ=255)                                                                    cAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCg                                                                                                                                                       <  1:258662/251‑1 (MQ=255)                                                                    cAGTTACCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGATAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTAACGAAAAGTGATTAAAAGGGAGCCAATACCGGCAAATCGTTGCGAATAAGGTAAAGGTTaacgtgagtaaaccg                                                                                                                                                       >  2:469902/1‑238 (MQ=255)                                                                             ttGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTACAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCt                                                                                                                                              >  1:163341/1‑251 (MQ=255)                                                                                                 aCCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTg                                                                                                                          >  1:307712/1‑251 (MQ=255)                                                                                                   cAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGtt                                                                                                                        <  1:11253/251‑1 (MQ=255)                                                                                                         aCCACGGCCAGCAACTGCACCATGGTAAGAAAATCTTTAGCAATAAAAATAGCCAAAGAGATCATCCACGGAGCAGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATACCGTCCTGGCGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCTTTGAGAATAAAGTGCAGGTGAAACTGGGTAAAGCGGCATCGGCTTATGGCCCTCAAGCGGCCTGTTTACgg                                                                                                                   <  2:87522/250‑1 (MQ=255)                                                                                                                    aaaCGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTa                                                                                                       <  2:146892/250‑1 (MQ=255)                                                                                                                                      cAAATATTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTtacat                                                                                      >  1:144562/1‑247 (MQ=255)                                                                                                                                           cTTTAGCAATAAAAATCGCCAACGAGATCATCCACACAGCCGTGTCTGGCGTCGAGTTAATACGAGAGAATAGAGAGAGATTAAAATTTGCAAGCATACCTTCCTGACGCAAGGTGATTCAAGGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGACGGTACAAATGGGTAAAGAGGCATAGTCTTATTTCACTCAAGGGACCTGTTTAGGGTTGGTGATTGTAAAGGGCAAAGGTtacataacaat                                                                                >  2:588766/1‑247 (MQ=255)                                                                                                                                                    tAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAAATGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTaaagaa                                                                         >  2:269558/1‑249 (MQ=255)                                                                                                                                                            gCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCta                                                               <  1:442798/251‑1 (MQ=255)                                                                                                                                                              cAACTAGATCATCCACGGAGCCTAGTCTGGCGTCTCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTTCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATGTCCCTCAAGCGGCCTGTTTACGGTTTGTGATTGTAACTGGCATAGGTTAAATAAAACGTAAAGAAAGCGTAGCtata                                                             <  1:598303/251‑1 (MQ=255)                                                                                                                                                                     atcatcCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGta                                                       >  1:186315/1‑250 (MQ=255)                                                                                                                                                                     atcatcCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATCTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTTGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGtaa                                                      <  1:378621/251‑1 (MQ=255)                                                                                                                                                                                                       taaGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCt                    >  1:661401/1‑251 (MQ=255)                                                                                                                                                                                                                         gaTTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCg  <  1:269558/251‑1 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                 GAAAAAGATGTCCCATCGTCCAGGACACAAACAGGCTGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCCGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCG  >  NC_000913/883154‑883620

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑