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	96.9%	104.5 / NA	32	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 (1/0);  new base T (14/17);  total (15/17)
Fisher's exact test for biased strand distribution p-value = 4.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGCGGAAAAAGATGTCCCATCGTCCAGGACACAAACAGGCTGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCCGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGC  >  NC_000913/883149‑883630                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                           gTGCGGAAAAAGATGTCCCATCGTCCAGGACACAAACAGGCGGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGAc                                                                                                                                                                                                                                         <  2:100975/251‑1 (MQ=255)         aaaGATGTCCCATCGTCCAGGACACAAACAGGCTTACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGATAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTg                                                                                                                                                                                                                                 <  1:183650/251‑1 (MQ=255)                       gTCCAGGACACAAAAAGGCTGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATGCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGcc                                                                                                                                                                                                                   <  2:21611/251‑1 (MQ=255)                           aGGACACAAACAGGCTGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATa                                                                                                                                                                                                               <  1:458477/251‑1 (MQ=255)                           aGGACACAAAAAGGCTGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATACCTTCCTGACGCCAAGCGATTAAAAGGGAGCCAAt                                                                                                                                                                                                                >  1:212124/1‑250 (MQ=255)                              acacAAACAGGCTGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAg                                                                                                                                                                                                            <  1:527491/251‑1 (MQ=255)                                  aaaCAGGCTGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCa                                                                                                                                                                                                         >  2:7634/1‑250 (MQ=255)                                  aaaCAGGCTGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCa                                                                                                                                                                                                         >  1:454270/1‑250 (MQ=255)                                           gACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGGTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAAGCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGAGTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGGCGTTg                                                                                                                                                                                                 <  1:77278/249‑1 (MQ=255)                                                                   tATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTggg                                                                                                                                                                        <  2:336332/250‑1 (MQ=255)                                                                                                        cAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGtt                                                                                                                                  <  2:326850/251‑1 (MQ=255)                                                                                                          aaGTACCACGGCCAGTAACGTAACCACGGTAATCAAATATTTAGCAATAAAAATCGGCAACGAGATCATCCACGGAGCCGAGTCGGGCTTCGCGTTAATAATAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGATAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGTCTGGTTa                                                                                                                                <  2:354749/251‑1 (MQ=255)                                                                                                                       aGCAACGGCTCCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCAAGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAAGAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTAGTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTg                                                                                                                   <  2:88308/251‑1 (MQ=255)                                                                                                                         cAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGGCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTGTACGGTGGGTGATTGTa                                                                                                                 <  1:3872/251‑1 (MQ=255)                                                                                                                          aaCGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGCGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTa                                                                                                                 >  1:520679/1‑250 (MQ=255)                                                                                                                              gCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACggg                                                                                                            <  2:463664/251‑1 (MQ=255)                                                                                                                                accacGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTAGTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCa                                                                                                          <  1:324987/251‑1 (MQ=255)                                                                                                                                               tCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGc                                                                                                                                          <  2:432448/204‑1 (MQ=255)                                                                                                                                               tCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGc                                                                                                                                          >  1:432448/1‑204 (MQ=255)                                                                                                                                                     gCAATAAAAAGCGCCAACGAGATCAAACACGGAGCAGAGTGTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCAAGCATAACGTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGAAAGTCGTTGAGAATAAAGTGCAGGATAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCGGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTaaag                                                                                     <  1:435728/251‑1 (MQ=255)                                                                                                                                                         tAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTaaagaa                                                                                   >  1:551973/1‑249 (MQ=255)                                                                                                                                                                            catccacaccgctaacactaaagTCGCGTTAATAAGAGCGACTAGAGAGAGAATCAAATTTTCCCCCATAAATACCCGACGCACCGTGATTAAAAGGGAGCCAATACAGGCCAGTCGTTGTGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCTTCAGGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATCGGTTAAATCAACCTTAAAGAAAGCGTACCTATACTCGtaat                                                               >  2:537946/23‑250 (MQ=255)                                                                                                                                                                                  cGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGACTAGAGAGAGCCTCAACTTTTCCAGCATAACTTCCTGACGGAAACTGGTTAAAAGGGAGCCAATCCAGGCAAGTCGTTGCGAATAACGCGCCGGTTAACCTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTCCGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTACAGAAAGCGTAGCTATACTCGTACTAATGTa                                                         >  1:223798/1‑250 (MQ=255)                                                                                                                                                                                       ccGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAAtg                                                   <  1:269600/251‑1 (MQ=255)                                                                                                                                                                                                  gTCGCGTTAATAAGAGAGAATAGAGCGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCCGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGGGGGTGATTGTAACGGGCATAGGTTAAATAACACTTAAAGAAAGCGTAGCTATACTCGTAATACTGTAAGAATGTGCTTAAcagt                                        >  1:435822/1‑248 (MQ=255)                                                                                                                                                                                                          aataaGAGAGAATAGAGAGGGATTCAACTATTCAAGCATAACTTCCTGACGAAAAGTGATTAAAAGGGAGCCAATACAGCCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATCACACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTACGAATGTGCTTAACCGTGGTTTc                                  >  2:550347/1‑249 (MQ=255)                                                                                                                                                                                                             aaGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCt                              >  2:414114/1‑250 (MQ=255)                                                                                                                                                                                                                     aTAGAGAGAGATTCAAATTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTc                     >  1:397840/1‑251 (MQ=255)                                                                                                                                                                                                                                     aTTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTg     >  1:213665/1‑251 (MQ=255)                                                                                                                                                                                                                                     aTTTTCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTg     <  1:7634/251‑1 (MQ=255)                                                                                                                                                                                                                                       tttCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTAAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTgcg   >  1:50409/1‑251 (MQ=255)                                                                                                                                                                                                                                        ttCCAGCATAACTTCCTGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTgcgc  >  1:135663/1‑251 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                           GTGCGGAAAAAGATGTCCCATCGTCCAGGACACAAACAGGCTGACCGCCAGCGCGATAGCGATTTTTATCACCAGTTGCCGTTGTGCTGTAAGCCCCCACAACCAAAGTACCACGGCCAGCAACGGCACCACGGTAATCAAATCTTTAGCAATAAAAATCGCCAACGAGATCATCCACGGAGCCGAGTCTGGCGTCGCGTTAATAAGAGAGAATAGAGAGAGATTCAAATTTTCCAGCATAACTTCCCGACGCAAAGTGATTAAAAGGGAGCCAATACAGGCAAGTCGTTGAGAATAAAGTGCAGGTTAAACTGGGTAAAGCGGCATCGTCTTATTTCCCTCAAGCGGCCTGTTTACGGTGGGTGATTGTAACGGGCATAGGTTAAATAAAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGC  >  NC_000913/883149‑883630

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑