Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	17,000	0	C	T	44.4%	66.3 / 24.2	54	intergenic (‑40/‑489)	mokC/nhaA	regulatory protein for HokC, overlaps CDS of hokC/sodium‑proton antiporter
Reads supporting (aligned to +/- strand):  ref base C (23/7);  new base T (0/24);  total (23/31)
Fisher's exact test for biased strand distribution p-value = 2.69e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCGGTGATACAGATGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTT  >  NC_000913/16850‑17148                                                                                                                                                       |                                                                                                                                                     ggcggTGATACAGATGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCATTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGc                                                                                                                                                      >  2:130412/1‑151 (MQ=255)  gcggTGATACAGATGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCt                                                                                                                                                     >  2:274272/1‑151 (MQ=255)          aCAGATGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTctct                                                                                                                                              <  2:1063264/150‑1 (MQ=255)                         ggCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTa                                                                                                                              <  1:725741/151‑1 (MQ=255)                           cGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAAt                                                                                                                            >  2:749946/1‑151 (MQ=255)                            gACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATg                                                                                                                           >  2:782198/1‑151 (MQ=255)                             aCAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGc                                                                                                                          >  2:1050180/1‑151 (MQ=255)                             aCAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGc                                                                                                                          >  2:167888/1‑151 (MQ=255)                              cAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGcc                                                                                                                         >  1:263643/1‑151 (MQ=255)                              cAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGcc                                                                                                                         >  2:708661/1‑151 (MQ=255)                                     cGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGagac                                                                                                                   <  2:989417/150‑1 (MQ=255)                                        cTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGagacagac                                                                                                               >  1:753592/1‑151 (MQ=255)                                         ttATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGagacagac                                                                                                               >  2:852342/1‑150 (MQ=255)                                              ctgctTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTc                                                                                                         >  1:663802/1‑151 (MQ=255)                                                   tCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGc                                                                                                     <  1:366296/150‑1 (MQ=255)                                                    cATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCAc                                                                                                   >  2:506095/1‑151 (MQ=255)                                                       tGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCAccc                                                                                                 <  1:1099343/150‑1 (MQ=255)                                                            tcttctCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCt                                                                                           >  2:151108/1‑151 (MQ=255)                                                             cttctCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCt                                                                                           >  2:237451/1‑150 (MQ=255)                                                                         cTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGctc                                                                               >  1:843625/1‑150 (MQ=255)                                                                              ggTAAGTAAGAGCCCCTCTACTTGTGTTCAGCATATAGGAGGCCTCGGTTTGATGGAAAAATACCCCTCGGGGTTTTTCTTTATCTCCCGTTCAGCTAATGCCTGAGACAGCCAGCCCCAAGCACCCGCCGCTATTATATCGCTCTCTTTa                                                                         <  1:1071453/151‑1 (MQ=255)                                                                              ggTAAGAAAGAGGCCCTCTACATTTTTTAAGCATATGGGGGCCCTGGGGTTGTTGAAAAAATATCCCCCGGTTTTTTTCTCTCCCGCCCTTTCAGTTACTCCCTGAGACAAACACCCTAAACCCCCCGCCGCTATTATATCGctctct                                                                            <  2:203168/148‑1 (MQ=255)                                                                              ggTAAGAAAGAGGCACTCTACATGTGTTCAGAATATGGGAGGCCTGGGTTTGATGAAAAAATATCCCGCGGGTTTTTTCTCTTTCTGCCGTTCAGATAAGGCCTGAGACAGACACCCCCAAGCACCCGCCGCTATTATATCGCTCTCttt                                                                          <  1:238994/150‑1 (MQ=255)                                                                                   gTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAAccc                                                                     >  2:261123/1‑150 (MQ=255)                                                                                         ggCACTCTACATGTGTTCAGCATATAGGAGGCCTGGGGTTGATGGAAAAATATCCCTGGGGGTTTTTCTCTATCTGCCTTTCAGCTAATGCCGGAGACAGACACCCCCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGt                                                              <  1:782176/151‑1 (MQ=255)                                                                                          gCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGtt                                                             >  2:996212/1‑151 (MQ=255)                                                                                             ctctACATGTGTTCAGCATATAGGGGCCCGGGGTTTGAGGAAAAAATACCCCTGGGGTTTTTTCTCTATCCCCTGTTCAATTATCCCCTGAGACAGACAGCTTCACGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGtttt                                                           <  2:840131/150‑1 (MQ=255)                                                                                              tctACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTAt                                                         >  2:60899/1‑151 (MQ=255)                                                                                                 actttttttaagaatatGGGGGCCCTGGGTTTGATGAAAAAATATCCCGGGGGTTTTTTCTCTATCTCCCGTTCATCTAAGGCCTGAGACACCCAGCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCAtttt                                                                <  2:633396/128‑1 (MQ=255)                                                                                                 aCATGTTTTCAGAATATAGGAGGCCTGGGTTTGATGAAAAAATATCACTCGGGGTTTTTCTCTTTCTGCCTTTCATCTAATGCCGGAGACAGACACCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCg                                                       <  1:921434/150‑1 (MQ=255)                                                                                                   aTGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGAtt                                                    >  1:86084/1‑151 (MQ=255)                                                                                                     gtgtTCAGCATATAGGGGGCCTGGGTTTGATGAAAAAATACCCCCCGGGGTTTTTCTCTATCGCCCGTTCAGCTAATGCCGGAGACAGACACCCTAAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGa                                                      <  1:127244/147‑1 (MQ=255)                                                                                                      ttttCAGAATAGGGGGGCCCTGGGGTTGATGAAAAAATATCCCTCGGGGTTTTTCTCTATCTGCCTTTCAGCTAATCCCTGAGACAGACACCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCt                                                  <  1:957721/148‑1 (MQ=255)                                                                                                        ttaaacATATGGGGGCCCGCGGGTTGATGAAAAAATCTCCCCCGGGGTTTTCCTCTTCCTGCCTTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGAtt                                                    <  2:663819/141‑1 (MQ=255)                                                                                                        tgcagtataagggagcCCTGGGTTTAATAATAAAATATCCCTCGGGTTTTTTCTCTCCCTGCTTTTAAGCTAATCCCTGACACACACACCCACAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTa                                                 <  2:250863/138‑1 (MQ=255)                                                                                                          cAGCATATGGGGGGCCGCGGTTTGATGGAAAAATACCACTGGGGGTTTTTCTCTATCTGCCTTTCATCTAATGCCTGAGAAAGCCAGCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCt                                                  <  2:381450/146‑1 (MQ=255)                                                                                                                   gggggCCTGGGGTTGATGATAAAATATCCCTCGGGGTTTTTCTCTATCTGCCGTCCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAg                                        <  1:274261/144‑1 (MQ=255)                                                                                                                   ggggcccTGGGTTTGATGAAAAAATACCCCGCGGGTTTTTTCTCTATCTCCCTTTCAGCTAATGCCTGAGACAGACACCCTCAACCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGc                                    <  2:676151/146‑1 (MQ=255)                                                                                                                   ggaggCCTGGGGTTGATGGAAAAATACCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCAGAGACAGACGCCCTCAATCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGAc                                      <  1:749927/149‑1 (MQ=255)                                                                                                                   ggaggCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGc                                    >  1:85048/1‑151 (MQ=255)                                                                                                                   ggaggCCTCGGGTTGATGATAAAATACCCCTCGGGGTTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACACCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACg                                     <  1:151098/150‑1 (MQ=255)                                                                                                                   ggagcCCTGGGTTTGAGGAAAAAATCCCCCTGGGGTTTTTTCTCTATCTGCCTTTCAGTTAAGCCCTGAAACACCCACCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGa                                       <  2:826221/148‑1 (MQ=255)                                                                                                                   ggagcCCTGGGGTTAAGGAAAAAATATCACTGGGGCCTTTTCTCTTTCTGCCGTTCAGCTAAGGCCAGAACCAGCCAGCCCCACCCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGAc                                      <  1:108722/149‑1 (MQ=255)                                                                                                                        ccTGGGGTTGATGGAAAAATATCACTCGGGGTTTTTCTCTTTCTGCCGTTCAGCTAATGCTTGAGACAGACAGCCCCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGc                               <  1:354973/151‑1 (MQ=255)                                                                                                                            gggTTGATGAAAAATTACCCCTGGGTTTTTTTCTCTTCCTCCCTTTAACCTAATGCCTGAGACAGCCACCCTCAACCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCAtt                            <  2:238182/150‑1 (MQ=255)                                                                                                                                       aaaaTATCCCTGGGGGTTTTTCTCTTTCTGCCGTTAAGCTAATGCCTGAGACAGACACCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTtg                        <  1:506089/143‑1 (MQ=255)                                                                                                                                       aaaaTATCCCTCGGGTTTTTTCTCTATCTCCCGTTCAGCTATGCCCTGAGACAGCCACCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGc                    <  1:764822/147‑1 (MQ=255)                                                                                                                                       aaaaTACCCCTCGGGTTTTTTCCTTCTCTGCCTTCCAGCTAATCCCTAAGAAAGACACCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTgg                     <  2:91557/146‑1 (MQ=255)                                                                                                                                       aaaaTACCACTCGGGTTTTTTCTCTATCTGCCTTTCAGTTAATGCCTGAAACAGACAGCCTAAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCAttttt                         <  2:577436/142‑1 (MQ=255)                                                                                                                                         aaTATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAAtt              >  1:496061/1‑151 (MQ=255)                                                                                                                                           tatCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAAtttt            >  2:384301/1‑151 (MQ=255)                                                                                                                                                  cGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATg      >  1:180998/1‑150 (MQ=255)                                                                                                                                                   ggggTTTTTCTTTATCTCCCTTTCAGCTATTGCCTGAGACAGACAGCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAAt       <  1:543732/148‑1 (MQ=255)                                                                                                                                                   ggggTTTTTCTCTATCTGCCTTTCAGCTAATGCCTGAGACAGACACCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAAt       <  1:167876/148‑1 (MQ=255)                                                                                                                                                     ggCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGAttt  >  2:814544/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                     GGCGGTGATACAGATGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATGATTT  >  NC_000913/16850‑17148

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑