Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,568,504	0	T	G	41.7%	63.5 / 13.9	49	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 (20/0);  total (27/22)
Fisher's exact test for biased strand distribution p-value = 1.62e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATC  >  NC_000913/4568367‑4568640                                                                                                                                          |                                                                                                                                           agGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCTTGGCGGGaaa                                                                                                                                          >  1:445412/1‑140 (MQ=255)     gCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTaaaaaa                                                                                                                                      >  2:359276/1‑140 (MQ=255)       cAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAc                                                                                                                                    >  1:549241/1‑140 (MQ=255)       cAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAc                                                                                                                                    >  1:332817/1‑140 (MQ=255)        aGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaaaaaaa                                                                                                                                   >  2:421549/1‑138 (MQ=255)             gACATCGGCATTAAAATCACGTACCACATTAATGATCTCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCa                                                                                                                             <  1:8125/140‑1 (MQ=255)             gACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCa                                                                                                                             <  1:51453/140‑1 (MQ=255)             gACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCa                                                                                                                             <  2:435691/140‑1 (MQ=255)             gACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCa                                                                                                                             >  1:435691/1‑140 (MQ=255)               cATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATa                                                                                                                           <  1:698254/140‑1 (MQ=255)                                  tACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCg                                                                                                        <  1:319336/140‑1 (MQ=255)                                  tACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCg                                                                                                        >  1:336891/1‑140 (MQ=255)                                     cacaTTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACATACAACTCCTTGTCCGga‑g                                                                                                    <  1:140291/140‑1 (MQ=255)                                            aTGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGA‑GGCATAAAAAAAAACACCTTGTCCGGA‑GAAccccc                                                                                             >  2:123500/1‑139 (MQ=255)                                                 cccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTc                                                                                                          <  2:132066/123‑1 (MQ=255)                                                 cccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAAAAAAAAAATCCTTGTCCGGA‑GAACCCCAACggg                                                                                        >  1:83196/1‑140 (MQ=255)                                                 cccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGT‑GGCATAACAAACAACTCCTTGTc                                                                                                          >  1:132066/1‑123 (MQ=255)                                                 cccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGAGAAAAAAAAGT‑AGCATAACAAAAAACTCACTGTCCCGA‑GAAACCCAAAggg                                                                                        >  1:409543/1‑140 (MQ=255)                                                  ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGT‑GGCATAACAAACAACTCCTTTTCCGGA‑GAACCCCAACcggg                                                                                       >  1:43086/1‑140 (MQ=255)                                                  ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGT‑GGCATAACAAAAAACTCCTTTTCCGGA‑GAACCCCCACgggg                                                                                       >  1:302503/1‑140 (MQ=255)                                                  ccAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGA‑GGCATAACAAACAACACCCTGTCCGGA‑GGACCCCAACcggg                                                                                       >  2:620992/1‑140 (MQ=255)                                                      gCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTGAAAAAAAAA‑GGCAAAAAAAACAAATCCCTGTCCGGA‑GAACCCCCACGGGGgaaa                                                                                   >  2:670696/1‑140 (MQ=255)                                                        tGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACg                                                                                 <  1:421549/140‑1 (MQ=255)                                                          gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGG‑GGGATAAAAAAAAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAAAGaa                                                                               >  2:101107/1‑140 (MQ=255)                                                          gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAACG‑GGGATAACAAAAAACTCCTTGTCCGGA‑GAAACCCAACGGGGGAAAAGaa                                                                               >  1:374485/1‑140 (MQ=255)                                                           aTCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGT‑GGCATAAAAAACAACACCCTGTCCGGA‑GAAACCCCACGGGGGAAAAGaaa                                                                              >  1:392360/1‑140 (MQ=255)                                                             cAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGG‑GGGATAACAAACAAATCCTTGTCCGGG‑GAACCCCAAAGGGGGAAAAGAAAtt                                                                            >  2:454506/1‑140 (MQ=255)                                                                 tCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAAt                                                                        <  2:336891/140‑1 (MQ=255)                                                                  ccGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGGAAACGAAAATCAATa                                                                       >  1:269198/1‑140 (MQ=255)                                                                   cGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATAc                                                                      <  1:359276/140‑1 (MQ=255)                                                                    gTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGACAAAAAACAG‑GGGGTAAAAAACAACCCCGTTCTCGGA‑GAAGCCCAACGGGGGAAAAGAAAATCAAGAcc                                                                     >  2:697346/1‑140 (MQ=255)                                                                     tCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGTGGGCAAAAAAAACAACCCCTT‑TCCCGC‑GAAACCCCACGGGGGGAAAAAAAATCAATAccc                                                                    >  2:542061/1‑139 (MQ=255)                                                                       gACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGT‑GGGATAAAAAACAACTCCTTTTCCGGA‑GAACCCCCACGGGGGAAAAGAAATTCAATACCGTc                                                                  >  1:203680/1‑140 (MQ=255)                                                                          aGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGG‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCggg                                                               >  1:348315/1‑139 (MQ=255)                                                                          aGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGG‑GGCATAAAAAAAAAAACCCTGTCCGGG‑GAACCCCAACGGGGGAAAAGAAAATCAAAACCGTCggg                                                               >  2:426303/1‑139 (MQ=255)                                                                          aGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGT‑GGCATAACAAACAACTCCTTGTCCGGG‑GAACCCCCACGGGGGAAAAGAAAATCAAAACCGCCggg                                                               >  2:407251/1‑139 (MQ=255)                                                                            aTACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTaa                                                             <  2:368385/140‑1 (MQ=255)                                                                                      aaGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGT‑GGCATAACAAAAAACTCCTTGTCCGGA‑GAACCCCCACGGGGGAAAAGAAAATCAATACCGGCGGTAATGACGaaaag                                                   >  2:431281/1‑138 (MQ=255)                                                                                             aCAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTga                                            <  2:549241/140‑1 (MQ=255)                                                                                               aaaaTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTgaga                                          <  1:353703/140‑1 (MQ=255)                                                                                                 aaTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAg                                        <  2:409543/140‑1 (MQ=255)                                                                                                 aaTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAg                                        <  1:426303/140‑1 (MQ=255)                                                                                                         ccATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACga                                <  1:670696/140‑1 (MQ=255)                                                                                                            tCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGG‑GGCATAAAAAACAACTCCCTGTCCGGG‑GGACCCCCACGGGGAAAACGAAAATCAATAACGTCGGGAATGACGAAAAGCAGGGGAGAAGGGGAACgagaa                             >  2:293681/1‑139 (MQ=255)                                                                                                             cGGGAAAAACAGCGTGGCGGCATGGCGGGTTTAAAAAAAT‑GGCAAAACAAACAAATCCTTGTGCGGATGACCCCCAAGGGGGAAACCCAATTTTAACA‑CGTGGGTAAGTACAGAAAGCAGGGGAGGAGGGCAAAGacacc                            >  2:334951/1‑139 (MQ=255)                                                                                                                      cAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTa                   <  1:123500/140‑1 (MQ=255)                                                                                                                         cGTGGCGGCATGGCGGGGAAAAAAAAGG‑GGCCTAACAAAAAACTCCTTGTCCGGA‑GAACCCCCACGGGGGAAACGAAAATCAATACCGGCGGGAAAGACGAAAGGCAGGGGAGAAGGGCAACGAGACTGCAAAAGTACTg                >  2:511674/1‑140 (MQ=255)                                                                                                                                gcATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCa         <  2:333609/140‑1 (MQ=255)                                                                                                                                    ggCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTa     <  2:305804/140‑1 (MQ=255)                                                                                                                                    ggCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTa     <  1:109543/140‑1 (MQ=255)                                                                                                                                      cGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAAt   <  2:392360/140‑1 (MQ=255)                                                                                                                                       gggTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATc  <  1:407251/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                           AGGGGCCAGACTGACATCGGCATTAAAATCACGTACCACATTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGT‑GGCATAACAAACAACTCCTTGTCCGGA‑GAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAAGGGCAACGAGACTGCAAATGTACTGAATTTCATGTAATC  >  NC_000913/4568367‑4568640

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑