Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	44.4%	82.9 / 17.1	54	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (23/7);  new base C (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

GCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTG  >  NC_000913/1376356‑1376652                                                                                                                                                      |                                                                                                                                                    gCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAacac                                                                                                                                                    >  2:768012/1‑151 (MQ=255)     aCCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCt                                                                                                                                                 <  1:41227/150‑1 (MQ=255)      ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCg                                                                                                                                               <  1:263460/151‑1 (MQ=255)        gccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGcc                                                                                                                                             <  1:855140/151‑1 (MQ=255)          cgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCg                                                                                                                                            >  2:626088/1‑150 (MQ=255)           gATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGAt                                                                                                                                          <  1:658034/151‑1 (MQ=255)             tGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATg                                                                                                                                         <  1:867503/150‑1 (MQ=255)             tGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGc                                                                                                                                        >  2:212150/1‑151 (MQ=255)              gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGcc                                                                                                                                       >  1:639376/1‑151 (MQ=255)               aCCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGccc                                                                                                                                      >  1:562653/1‑151 (MQ=255)                   cgccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCccgcc                                                                                                                                   <  1:333895/150‑1 (MQ=255)                          tAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtc                                                                                                                           >  2:137977/1‑151 (MQ=255)                             ccgggAGGGCGACCGAAAAAGGGGGAGTGATTCCCGGCGCGTACGGGAACAGGTCGCCGCGCGTCCCGGAACCGTGGTGTATCTCGAACCGTTAACCCCCTATAAGTATCATATGATAAACCCCCTCGCCGATGCCCGCCGTTACAtc                                                                                                                           <  1:173959/145‑1 (MQ=255)                                  aCGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGaa                                                                                                                     >  1:600356/1‑149 (MQ=255)                                   cGGCGACCGCAAAATGGTGAGTGATTCCCTGCGTGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAAc                                                                                                                  >  2:789805/1‑151 (MQ=255)                                   cGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAAc                                                                                                                  >  1:617945/1‑151 (MQ=255)                                    ggCGACCAAAAATTGGTGAGTGATTCCCTGCGCGTCCGGGAACGGGCCGCGGCGCGTCCCGGACCCGGGTTATTGCGCGAACCGTAAACCCGCTGTAAGGATTATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAAc                                                                                                                  <  2:916499/150‑1 (MQ=255)                                       gaccaaaaaaTGGGGAGTGATCCCCGGCGGGTACTGAAACAGGCCGCCGCGCGTACCGGACCGGTGTTGTATCTCGACCGGTAAACCCGCTATCGGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGAt                                                                                                               <  2:951734/144‑1 (MQ=255)                                         ccGAAAAAGGGGGAGTGATTCCCTGCGCTTACGGAAACAGGCCGCCGCGCGTCCCGGAACCGTGGTTTATCCCGACCCTTAAACCCCCTACCAGGATCATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                            <  1:978195/151‑1 (MQ=255)                                             aaaaTGGTGAGTGTTTCCCTGCGCTTACTGGAACGGGTCGCCGCGCGTACCGGACCGGGGGTGTATCTCGACCCTTAAACCCGCTATAAGGATCATATGACCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTa                                                                                                           <  1:811900/148‑1 (MQ=255)                                               aaTGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGCGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTaa                                                                                                          >  1:207379/1‑147 (MQ=255)                                                        tgaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                             >  1:538880/1‑151 (MQ=255)                                                             cccTGCGCGTACTGGAACGGGTCGCCGCGCTTACCGGACCCGTGTTGTATCTCGACCCGTTAAACCGCTATCAGGATCATATAATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                             <  1:191852/146‑1 (MQ=255)                                                             cccTGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGGACCCGTGGTGTATCTCGACCCGTTAACCCGCTATCAGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                           <  2:453479/148‑1 (MQ=255)                                                                 gcgcGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAt                                                                                    >  2:312711/1‑151 (MQ=255)                                                                  cgcgTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAtt                                                                                   >  1:912714/1‑151 (MQ=255)                                                                      tACGGGAACAGGTCGCCGCGCGTCCGGGAGCCGGGGTTTTCCGCAAACGTTTAACCCGCTATGAGAACAATATGATCACCACCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTc                                                                                 <  1:950483/149‑1 (MQ=255)                                                                               agtccgccgcGCGGACCGGAACGGTGGTTTATCTCGACCCTTTAACCCGCTATAAGTATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcaca                                                                          <  1:632541/143‑1 (MQ=255)                                                                                gttCGCCGCGCGCCCGTGACCCGTGGTTTCTCTCGACCCATTAACCCCTTTTGAGGATCATATAATCAACCCCCCCGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATg                                                                        <  1:911312/146‑1 (MQ=255)                                                                                ggccgccgcGCGTCCCGAAACCGTGTTTTATCCCAACCCTTTAACCCGCTATCAGGATCATATAAACAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAat                                                                     <  1:476830/148‑1 (MQ=255)                                                                                ggTCGCCGCGCGTACCGGACCCGTGGTGTATCTCGAACCGTTAACCCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGaa                                                                      <  2:430495/150‑1 (MQ=255)                                                                                ggTCGCCGCGCGTACCGAAACGGGGTTTTATCCCGACCCTTAAACCCGCTATCAGAATCATATGACAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGaa                                                                      <  1:523781/150‑1 (MQ=255)                                                                                  tCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAatat                                                                   >  1:190928/1‑151 (MQ=255)                                                                                         gcgTACCGGACCCGTGGTGTACCTCGACCCTTTAACCCCCTATCAGGATAATATGATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaag                                                              <  1:977561/149‑1 (MQ=255)                                                                                         gcgTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                             >  1:714398/1‑150 (MQ=255)                                                                                              ccGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                             <  1:405890/145‑1 (MQ=255)                                                                                              ccGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATa                                                        >  2:258891/1‑150 (MQ=255)                                                                                                ggAACGGTGGTGTATCTCGAACCGTTAACCCGCTATCAGTATCATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                                     <  1:940878/151‑1 (MQ=255)                                                                                                   aCCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                                  >  1:8877/1‑151 (MQ=255)                                                                                                    ccGTGGTGTATCTCGACCCGTTAACCCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                                  <  2:236158/150‑1 (MQ=255)                                                                                                        ggtgTTTCTCCACCCTTAAACCCGCTAAAAGGGTAATATAATAAACCCCCCCGCTGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcg                                                <  1:690937/148‑1 (MQ=255)                                                                                                            tATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgcgc                                         >  2:526122/1‑151 (MQ=255)                                                                                                                   acccGTTAAACCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGa                                  <  2:122341/149‑1 (MQ=255)                                                                                                                        ttAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAcc                             >  1:179790/1‑151 (MQ=255)                                                                                                                          aacccGCTATCAGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgc                           <  2:138477/148‑1 (MQ=255)                                                                                                                           acccccTATCAGAATAATAAGACAACCCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgcg                          <  1:767927/146‑1 (MQ=255)                                                                                                                                  aTCAGGATAAAATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGTGCAGGCGCTGCATGACAACCGCGACCt                      <  1:942018/148‑1 (MQ=255)                                                                                                                                    cAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCg                 >  2:648589/1‑151 (MQ=255)                                                                                                                                      ggATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGt               >  2:108066/1‑151 (MQ=255)                                                                                                                                      ggATCATAGAATCAACCCCCGCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCgg                <  1:276150/150‑1 (MQ=255)                                                                                                                                        aTCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTc              >  2:641992/1‑150 (MQ=255)                                                                                                                                            tatGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCa             <  2:986969/147‑1 (MQ=255)                                                                                                                                             atGATCAACCCCCGCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATAGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg           <  2:921090/148‑1 (MQ=255)                                                                                                                                              tGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGc        >  1:158984/1‑150 (MQ=255)                                                                                                                                                   aaCACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTg  >  1:702044/1‑151 (MQ=255)                                                                                                                                                      |                                                                                                                                                    GCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTG  >  NC_000913/1376356‑1376652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑