Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,568,504	0	T	G	44.0%	65.0 / 11.4	51	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
Reads supporting (aligned to +/- strand):  ref base T (6/22);  new base G (22/0);  total (29/22)
Fisher's exact test for biased strand distribution p-value = 5.24e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCA  >  NC_000913/4568379‑4568641                                                                                                                              |                                                                                                                                             gACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCa                                                                                                                                <  1:391729/140‑1 (MQ=255)  aCATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACCTgggaa                                                                                                                               >  1:689495/1‑137 (MQ=255)   cATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATa                                                                                                                              <  1:374778/140‑1 (MQ=255)   cATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAATGGCATa                                                                                                                              >  2:81169/1‑140 (MQ=255)      aggCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaaca                                                                                                                           <  1:137733/139‑1 (MQ=255)        gCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGAGGCATaaaaaa                                                                                                                         >  2:374778/1‑140 (MQ=255)         cATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaacaaac                                                                                                                        <  1:64975/140‑1 (MQ=255)               aaTCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTcc                                                                                                                  <  2:526347/140‑1 (MQ=255)               aaTCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTcc                                                                                                                  <  2:236958/140‑1 (MQ=255)                   aCGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAACGGCATAACAAAAAACTCCttct                                                                                                              >  2:137733/1‑138 (MQ=255)                                  gATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTCAAAAAATGAGGCATAAAAAAAAAATCCTTT‑TCCGGAGAATCCCC‑aa                                                                                             >  1:306303/1‑140 (MQ=255)                                     cccAGGCTGGATCAGATCGGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGCAAAAAAAAGAGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACagg                                                                                         >  1:783152/1‑140 (MQ=255)                                     cccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCATAAAAAACAACTCCTTG‑TCCGGGGAA‑CCCC‑AACggg                                                                                         >  2:411491/1‑140 (MQ=255)                                      ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGGGGCATAAAAAACAACTCCTTG‑TCCGGGGGA‑CCCC‑CAAgggg                                                                                        >  1:202487/1‑140 (MQ=255)                                      ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACgggg                                                                                        >  1:10182/1‑140 (MQ=255)                                      ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGCGAAAAAACGGGGCATAACAAACAAATCCCTG‑TCCGGATAA‑ACCC‑CAAgggg                                                                                        >  1:302666/1‑140 (MQ=255)                                        aGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAACTCCTTT‑TCCCGAGAA‑ACCC‑AACggggga                                                                                      >  2:331764/1‑138 (MQ=255)                                        aGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGAGAAAAAAACGGCGGATTACAAACAAATTCTTG‑TTCGGAGAACCCCC‑AACGGGGa                                                                                       >  2:759193/1‑140 (MQ=255)                                         ggCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGTGGCATAAAAAAAAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGTGGaaa                                                                                     >  1:759959/1‑140 (MQ=255)                                          gCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGTGGCGTAACAAAAAAAACCTTG‑TCCCGAGAA‑CCCC‑AACGGGGgaaa                                                                                    >  2:751334/1‑140 (MQ=255)                                          gCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGAGGCATAAAAAACAACACCTTT‑TCCCGAGAA‑ACCC‑CACGGGGgaaa                                                                                    >  2:181902/1‑140 (MQ=255)                                            tGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACg                                                                                  <  1:181902/140‑1 (MQ=255)                                            tGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACg                                                                                  <  2:719890/140‑1 (MQ=255)                                              gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGGGGCAGAACAAAAAAACCCCTC‑TCCGGTGGA‑GCCC‑CACGGGGAAAAccca                                                                                >  2:310874/1‑137 (MQ=255)                                              gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAACAAACCCTTGTTCTGTAGAC‑CCCC‑AAGGGGAaaaaaaa                                                                                 >  2:676079/1‑137 (MQ=255)                                               aTCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGaaa                                                                               >  1:35535/1‑140 (MQ=255)                                               aTCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGTGGCATAAAAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGaaa                                                                               >  1:598484/1‑140 (MQ=255)                                               aTCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAACAACTCCTTT‑TCCGGAGAA‑CCCC‑CACGGGGAAAAAGaaa                                                                               >  1:629430/1‑140 (MQ=255)                                               aTCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGCGGCATAACAAAAAAACCCCTG‑TCCGGGGAA‑CCCC‑CACGGGGGAAAAGaaa                                                                               >  2:685446/1‑140 (MQ=255)                                               aTCAGATCCATCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGGAAAAGaaa                                                                               >  1:653504/1‑140 (MQ=255)                                                    aTCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGATAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCaa                                                                          >  2:255335/1‑140 (MQ=255)                                                     tCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAAt                                                                         <  1:685446/140‑1 (MQ=255)                                                         tCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGGGGGATAACAAAAAACTCCTTT‑TCCGGGGAA‑ACCC‑CACGGGGGAAAAGAAAATCAATaacc                                                                     >  2:506450/1‑137 (MQ=255)                                                         tCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCATAAAAAACAAATCCCTT‑TCCGGAGAA‑CCCC‑CACGGGGGAAACGAAAATCaaaaacc                                                                     >  2:589949/1‑135 (MQ=255)                                                         tCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAATGGCATAACAAAAAACTCCTTG‑TCCCGGGAA‑CCCCAAACGGGGAAAA‑AAAATTTAATACCg                                                                     >  2:751400/1‑140 (MQ=255)                                                              aGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCATAAAAAACAACTCCTTG‑TCCGGAGAA‑ACCC‑AACGGGGGAAAAGAAATTCAATACCGTCggg                                                                >  2:774237/1‑139 (MQ=255)                                                                   cGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGCGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGACAA‑CCCC‑AACCGGGAAAACGAAATTCAATACCGTCGGTAATGa                                                           <  2:754028/140‑1 (MQ=255)                                                                        caAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAAATCAATACCGTCGGTAATGACGaaa                                                      >  1:556190/1‑140 (MQ=255)                                                                          aaGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGTGGCATAAAAAAAAACCCCTTG‑TCCGGGGAA‑CCCC‑AACGGGGGAAAAGAAATTCAATACCGTCGGTAATGACGaaaag                                                    >  2:365280/1‑138 (MQ=255)                                                                           aGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑CACGGGGGAAAAGAAAATCAAAACCGTCGGGAAAGACGAAAAGc                                                   >  2:685009/1‑140 (MQ=255)                                                                             tCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAg                                                 <  1:411491/140‑1 (MQ=255)                                                                                   aaaaTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTgaga                                           <  1:751400/140‑1 (MQ=255)                                                                                   aaaaTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTgaga                                           <  1:751334/140‑1 (MQ=255)                                                                                       tCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAAATCCCTG‑TCCGGAGAA‑CCCC‑CACGGGGGAAACGAAAATCAAAACCGTCGGGAAAGACGAAAAGCAGGGGGGAAggg                                       >  2:405193/1‑140 (MQ=255)                                                                                           cGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAAc                                   <  1:69565/140‑1 (MQ=255)                                                                                                             cGTGGCGGCATGGCGGGGAAAAAAACGTGGCATAACAAACAACTCCCTG‑TCCGGAGAA‑CCCC‑CACGGGGGAAACGAAATTCAATACCGTCGGGAATGACGAAAGGCAGGGGGGAAAGGCAACGAGACTGCAAAAGTACTg                 >  2:75280/1‑140 (MQ=255)                                                                                                                      aTGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATTACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATg        <  1:81169/140‑1 (MQ=255)                                                                                                                      aTGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATg        <  2:35535/140‑1 (MQ=255)                                                                                                                      aTGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATg        <  1:506450/140‑1 (MQ=255)                                                                                                                      aTGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATg        <  1:75280/140‑1 (MQ=255)                                                                                                                      aTGGCGGGTAAAAAAACATGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATg        <  1:763841/140‑1 (MQ=255)                                                                                                                       tGGCGGGGAAAAAAAAGGGGCATAACAAAAAACTCCTTG‑TCCGGAGAA‑ACCC‑CACGGGGGAAAAGAAATTTAAAACCGTCGGGAATGACGAAAAGGAGGGGGGAAGGGGAAAGAGACTGCAAAATTACTGAATTTCATGt       >  2:79639/1‑140 (MQ=255)                                                                                                                        ggCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTa      <  1:589949/140‑1 (MQ=255)                                                                                                                        ggCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTa      <  1:759193/140‑1 (MQ=255)                                                                                                                           gggTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATc   <  1:685009/140‑1 (MQ=255)                                                                                                                            ggTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCa  <  2:560531/140‑1 (MQ=255)                                                                                                                              |                                                                                                                                             GACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTG‑TCCGGAGAA‑CCCC‑AACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATCA  >  NC_000913/4568379‑4568641

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑