Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	17,000	0	C	T	46.9%	44.6 / 26.8	49	intergenic (‑40/‑489)	mokC/nhaA	regulatory protein for HokC, overlaps CDS of hokC/sodium‑proton antiporter
Reads supporting (aligned to +/- strand):  ref base C (16/10);  new base T (0/23);  total (16/33)
Fisher's exact test for biased strand distribution p-value = 1.66e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCGGTGATACAGATGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATG  >  NC_000913/16850‑17144                                                                                                                                                       |                                                                                                                                                   ggcggTGATACAGATGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGc                                                                                                                                                    >  2:537412/1‑151 (MQ=255)        aTACAGATGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTt‑c‑tc                                                                                                                                           >  1:718433/1‑151 (MQ=255)           cAGATGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTAt                                                                                                                                        <  2:593715/151‑1 (MQ=255)              aTGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTg                                                                                                                                     >  2:989347/1‑151 (MQ=255)                      cAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTc                                                                                                                               >  2:409032/1‑149 (MQ=255)                      cAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCa                                                                                                                              <  1:620295/150‑1 (MQ=255)                        gggCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCt                                                                                                                           >  2:334728/1‑151 (MQ=255)                               aaTCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCt                                                                                                                    >  2:993972/1‑151 (MQ=255)                                     cGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGagaca                                                                                                              <  1:545621/151‑1 (MQ=255)                                       ccTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGagacaga                                                                                                            <  1:182033/151‑1 (MQ=255)                                       ccTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGagac                                                                                                               >  1:265091/1‑148 (MQ=255)                                          tATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGagacagac                                                                                                           <  1:1012374/149‑1 (MQ=255)                                          tATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGagacagac                                                                                                           >  1:42532/1‑149 (MQ=255)                                                gctTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCa                                                                                                    <  1:644273/150‑1 (MQ=255)                                                  ttCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGc                                                                                                 >  2:404799/1‑151 (MQ=255)                                                     aTTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCAc                                                                                               >  2:682838/1‑150 (MQ=255)                                                           ctctTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCcgccgc                                                                                        >  2:965692/1‑151 (MQ=255)                                                                   cTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTatat                                                                                >  1:555032/1‑151 (MQ=255)                                                                          ttACGGTCAGAAAGAGCCCCTCTAAATGTGTTCAACATAGGGGGGGCCTCGGTTTGATGGTAAATTATCCCTGGGGTTTTTT‑C‑CCTACCTGCCTTTCATCAAATGCTGGAGACAGACACCCCCAAGCACCCGCCGCTATTATATc                                                                               <  1:634558/145‑1 (MQ=255)                                                                                   gTAAGAGGCACTCTACATTTGTTCAACAAATGGGGGGCCTGGGTTTGATGAAAAAATATCACTGGGGTTTTTT‑C‑TCTATCTCCCTTTAACATATTCCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAAc                                                                   <  1:666991/148‑1 (MQ=255)                                                                                     aaGGGGCACTCTACATGTGTTCAGCATATAGGGGGCCTGGGGTTGAGGGAAAAATATCCCTCGGGTTTTTT‑C‑TTTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAAcc                                                                  <  1:303408/147‑1 (MQ=255)                                                                                       gggccACTCTACATTTTTCAACCATATAGGGGGCCTGGGTTTGATGGTAAAATACCACTCGGGTCTTTT‑C‑TCTATCTGCCTTTAATTTAATGCCTGAAACAGACACCCTAAAGCCGCCGCCGCTATTATATCGCTCTCTTTAACCCAtttt                                                            <  2:321659/147‑1 (MQ=255)                                                                                       gagCCACTCTCCATGTGTTAAGCATAGAGGGGGCCGGGGGTTGATGAAAAAATACCCCTGGGGTTTTTT‑C‑TCTTCCTCCCTTTCAGCTAATCCCTGAGACAGCCACCCACAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCAttt                                                             <  1:545117/150‑1 (MQ=255)                                                                                         ggCACTCTACTTTTTTTAAGAAAATAGGGGCCCTGGGGTGAATGGAAAAATACCCCTCGGGTTTTTT‑C‑TCTACCTCCCTTTCATCTAAGCCCTGAGACAGACGCCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGt                                                          <  1:648930/151‑1 (MQ=255)                                                                                         ggCACTCTACATGTTTTCAGCATATAGGAGCCCTGGGGTTGATGAAAAAATATCCCTCGGGTTTTTT‑C‑TCTTTCTCCCTTTCAGCTAATCCCTGAGACAAACACCCTAAACCACCCGCCGCTATTATATCGCTCTCTTTAACCCAtttt                                                            <  1:965656/149‑1 (MQ=255)                                                                                           ccctctACATGTTTTCAGAATATGGGAGGCCTCGGGTTGATGAAAAAATATCCCTCGGGTTTTTT‑C‑TCTTTCTGCTGTTAAATAAATGCCTGAGAAAGACAGCTTAAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGt                                                          <  1:547508/147‑1 (MQ=255)                                                                                                 aCATGTTTTCAGTATATAGGAGCCCCCGGTTTGATGAAAAAATATCGCT‑GGGGCTTTTCC‑TCTATCTGCCTTTCAAAAAACCCCTGAGACAGACACCCTCAGCCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCg                                                   <  2:63101/150‑1 (MQ=255)                                                                                                 aCATGTGTTCAGCATAAAGGAGGCCGGGGGTTGATGAAAAAATATCCCGCGGGGTTTTT‑C‑TTTTTCTCCCTTTTATTTAATCCCTGAGACAGCCATCCTCAACCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTAt                                                     <  1:565190/148‑1 (MQ=255)                                                                                                      ttttCAGAATAGGGGGGCCCTGGGTTTGATGAAAAAATACCCCTGGGGTTTTTT‑C‑TCTACCTCCTTTTCAGCTATTCCCGGAGACACCCAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTa                                                      <  1:273537/140‑1 (MQ=255)                                                                                                      tgtTCAGCATATAGGAGCCCTCGGGTTGATGGAAAAATATCCCTCGGGGTTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACACCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCt                                              <  2:718185/150‑1 (MQ=255)                                                                                                       gtTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTa                                             >  1:598781/1‑150 (MQ=255)                                                                                                        ttaagaatatAGGAGCCCTGGGTTTGATGTAAAAATACCCCCGGGGGTTTTT‑C‑TCTACCTGCCTTTCAGTTAATCCCTGAGACAGCCAGCCTCAACCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGAtt                                                <  1:502287/140‑1 (MQ=255)                                                                                                           aGCATATAGGAGGCCTCGGGTGGATGATAAAATATCCCTCGGGGTTTTT‑C‑TCTATCTGCCTTTCACTTAATCCCTGAGACAGACACCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCt                                        <  2:358825/151‑1 (MQ=255)                                                                                                                  aggagcCCGGGGTTTGATGAAAAAATACCCCTGGGGTTTTTT‑C‑TCTTCCTCCCTTTCAGTTAATCCCTGAGACAGACACCCTAAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGa                                   <  1:408995/149‑1 (MQ=255)                                                                                                                       gCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCg                            >  1:625783/1‑151 (MQ=255)                                                                                                                           cGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCAtt                        >  1:389849/1‑151 (MQ=255)                                                                                                                            ggttggaggtaaaaaTATCGCT‑GGGGCTTTT‑CTTCTATCTCCTGTACAGTAAATGCCGGAGAAAGACGGCCTCAGCCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCg                            <  1:770363/135‑1 (MQ=255)                                                                                                                            gggTTGATGGAAAAATACCCCTCGGGGTTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCa                          <  2:992690/148‑1 (MQ=255)                                                                                                                            gggTTGATGGAAAAATACCCCTCGGGGTTTTT‑C‑TCTATCTCCCGTTCAGCAATTGCCTGAGACAGACACCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCa                          <  2:830627/148‑1 (MQ=255)                                                                                                                             gtttGATGGAAAAATATCACTGGGGTTTTTT‑C‑TCTCTCTGCCGTTCAGCTAATGCCTGAGACAAACATCCTAAACCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCAt                         <  1:467452/146‑1 (MQ=255)                                                                                                                                 gATGGAAAAATATCACTGGGGGTTTTT‑C‑TCTATCTCCCGTTCAGCTAATGCCTGAGACAGACACCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTtgt                   <  2:625798/150‑1 (MQ=255)                                                                                                                                   gggTAAAATGCCCCGCGGGTCTTTT‑C‑TCTAGCTGCCGTTCGGTTAAGGCCTGAGAACGACAGCCTATAGCTCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTGTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTgg                 <  1:208505/149‑1 (MQ=255)                                                                                                                                       aaaaTCTCACTGGGGTTTTTT‑C‑TCTATCTGCCTTTCAGCTAATGCCTGAGACAGACACCCTAAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTaa            <  1:776310/151‑1 (MQ=255)                                                                                                                                       aaaaTATCCCTCGGGGTTTTT‑C‑TCTATCGGCCGTTCAGCTAATGCCTGAGACAGACACCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTtgt                   <  2:561996/144‑1 (MQ=255)                                                                                                                                        aaaTATCCCTGGGGGTTTTT‑C‑TCTTTCGGCCTTTCAGCTAATGCCTGAGACAGACACCCTCAACCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAAt           <  2:879516/151‑1 (MQ=255)                                                                                                                                         aaTATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAAtt          >  2:462771/1‑151 (MQ=255)                                                                                                                                          atatCCCTGGGGGTTTTT‑C‑TCTATCTGCCTTTCACCTAATGCTGGAGACAGACGCCCTAACGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAAtt          <  1:901150/150‑1 (MQ=255)                                                                                                                                              cccTCGGGTTTTTT‑C‑TCTCTCGGCCTTAAAGCTATTCCTAGAGAAAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAAtttt        <  1:667060/146‑1 (MQ=255)                                                                                                                                                 tCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATg  >  1:780613/1‑151 (MQ=255)                                                                                                                                                   ggggTTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCCCCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATg  <  2:776977/149‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                   GGCGGTGATACAGATGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTCTCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTGATGGTAAAATATCACTCGGGGCTTTT‑C‑TCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAGCACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCGCATTTTTGTGGCGTAATTTTTTAATG  >  NC_000913/16850‑17144

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑