Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	43.9%	84.2 / 22.9	57	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (23/9);  new base C (0/25);  total (23/34)
Fisher's exact test for biased strand distribution p-value = 6.48e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGT  >  NC_000913/1376359‑1376644                                                                                                                                                    |                                                                                                                                            tACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACAcc                                                                                                                                           <  2:191048/149‑1 (MQ=255) tACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACAcc                                                                                                                                           <  2:521171/149‑1 (MQ=255)   ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                        <  2:335370/150‑1 (MQ=255)   ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCg                                                                                                                                       <  1:401515/151‑1 (MQ=255)    cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGc                                                                                                                                      <  2:663680/151‑1 (MQ=255)    cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGc                                                                                                                                      >  1:221109/1‑151 (MQ=255)      ccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCg                                                                                                                                    <  1:959960/151‑1 (MQ=255)           gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGcc                                                                                                                               <  1:66238/151‑1 (MQ=255)            aCCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGccc                                                                                                                              <  2:961874/151‑1 (MQ=255)             ccTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCccg                                                                                                                             >  1:1018682/1‑151 (MQ=255)                  ccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCTACCCGTTAAACCGCTATCAGGATCATATGACCAACCCCCTCGCCGATGCccgccg                                                                                                                          <  2:575680/149‑1 (MQ=255)                      gTAGCCGGGACGGCACCCGAAAAATGGTGAGTTATCCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGGAA‑CCGGGGTGTATCTCAACCCTTTAAACCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACAt                                                                                                                    <  2:1093122/151‑1 (MQ=255)                       tAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtc                                                                                                                   >  1:758717/1‑151 (MQ=255)                        aGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtcg                                                                                                                  >  2:1089055/1‑151 (MQ=255)                                 ggCGACCGCAAAAGGGGGAGTGATCCCCTGCGCTTACTGGAACAGGTCGCCGCGCGTACCGGAC‑CCGGGGTTTTCCCCAACCCTTTAACCCCCTATCAGGATAATATAACCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACg                                                                                                         <  1:521735/151‑1 (MQ=255)                                     aCCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCt                                                                                                     >  2:624541/1‑151 (MQ=255)                                     aCCGAAAAATGGTGAGTGTTCCCCTGCGCTTATTGGAACGGTTCGCCGCGCTTCCCGGAC‑CCGTGGTGTTTCTCAACCCGTAAACCCCCTATCAGGATCATATGACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATc                                                                                                      <  2:972478/150‑1 (MQ=255)                                      ccGCAAAAGGGTGAGTGATCCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGAAC‑CCGGGGTGTATCCCGAACCTTTAACCCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGAt                                                                                                       <  2:307083/148‑1 (MQ=255)                                      ccGAAAAAGGGTGAGTGTTTCCCTGCGCGTCCTGAACCGGGCCGCCGCGCGTACCGGAC‑CGGTGGTGTACCTCGACCCTTTAACCCCCTATAAGAATAATATAACCACCCCCCCCCCCAATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                    <  1:641275/151‑1 (MQ=255)                                          aaaaTGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAAc                                                                                                >  2:966279/1‑151 (MQ=255)                                          aaaaGGGGGGGTGATCCCCTGCGCGTACGGGAACGGGCCGCCGCGCGTCCCGGAA‑CGGTGGTTTTTCTCGACCCTTAAACCCCCTATCAGGATAATATGATAACCCCCCTCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                    <  1:150173/147‑1 (MQ=255)                                           aaaTGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAAc                                                                                                >  1:184782/1‑150 (MQ=255)                                                  gtttgttccccTGCGCGTCCGGGAACAGGTCGCCGGGCGTCCGGGAC‑CCGTGTTTTATCCCAACCCGTAAACCCGCTTCAAGGACAATATAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACa                                                                                         <  1:342995/142‑1 (MQ=255)                                                    gtgaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                          >  2:191865/1‑147 (MQ=255)                                                    ggtttccccTGCGGGTCCAGGACCAGGTCCCCGCGCGACCGGGAA‑CCGTGTTGTACCCCGACCCGTTAAACCGCTTTCAGGAACATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAt                                                                                      <  1:91413/145‑1 (MQ=255)                                                      gtttCCCGGCGCGTCCGGAAAAGGGTCCCCGCGCGTCCGGGAC‑CCGTGGTGTACCTCAAACCTTTAACCCGCTATCAGGATCATAGGAAAAACCCCCTCGCCGTTCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                     <  2:933602/148‑1 (MQ=255)                                                      gaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                     >  1:308960/1‑150 (MQ=255)                                                          cccggggcgTACTGGAACAGGTCGCCGCGCGTCCCGGAA‑CCGGGGTGTATCTCAAACCTTTAACCCCTTATCGGGATAATATGATCAACCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATc                                                                                  <  2:1128018/143‑1 (MQ=255)                                                          cccGGCGCTTACGGGAACAGGGCCCCGCGCGCCCCGGAA‑CCGGGGTGTATCCCGACCCTTAAACCCGCTATCAGGATAATATAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATc                                                                                  <  1:398070/149‑1 (MQ=255)                                                           ccTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGc                                                                               >  2:3112/1‑151 (MQ=255)                                                                gcttACGGGAACAGGTCGCCGCGCTTCCCGGAC‑CGGTGGTGTATCGCGAACCTTTAACCCGCTATCGGGATCATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAt                                                                            <  2:101436/146‑1 (MQ=255)                                                                gcgTACTGGAACGGGTCGCCGCGCGTCCGGGAC‑CGGGGGTGTATCTCGACCCTTTAACCCGCTATCAGGATCATATGACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAt                                                                            <  2:34608/149‑1 (MQ=255)                                                                  ctacgtgAACGGCTCGCCGGGCGTACCGGAC‑CGGTGTTGTCCCGCGAACCGTTACACCGATAACAGGACCATATAATACACACCTTCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                          <  1:491885/143‑1 (MQ=255)                                                                   tccggaaaCAGGTCCCCGCGCGAACCGGAA‑CGGGGGTGTATCTCGAACCTTAAACCCGCTATCAGGATAATATAATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTc                                                                         <  1:638064/143‑1 (MQ=255)                                                                     cgggaccgggTCGCCGGGCG‑ACCGGAACCCGTGGTTTATCCCTACCCTTAAAACCTCAAACGGAATAATAGAACCACCCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGa                                                                             <  1:59418/135‑1 (MQ=255)                                                                                cgccgcGCGTCCGGGAC‑CCGTGGTGTATCGCGACCCGTTAACCCGATAACAGGATCATAAGAACAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAata                                                            <  2:673797/149‑1 (MQ=255)                                                                                      gcgTACCGGAC‑CCGGGGTTTATCTCGAACCGTTAACCCCCTATCAGGATCATATAATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaag                                                      <  2:388886/149‑1 (MQ=255)                                                                                               aa‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                           >  1:469258/1‑151 (MQ=255)                                                                                                acccGTGGTGTATCTCGACCCGTAAACCCGCTATCAGGATAATATGATAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCt                                            <  2:773198/148‑1 (MQ=255)                                                                                                a‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                          >  1:1046465/1‑151 (MQ=255)                                                                                                  ccGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                          >  2:995281/1‑150 (MQ=255)                                                                                                  ccGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgc                                         >  2:362364/1‑151 (MQ=255)                                                                                                    gtggtgTATCTCGAACCTTTAACCCGTTAAAAGAATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcg                                        <  2:719863/150‑1 (MQ=255)                                                                                                    gtggtgTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcgc                                       >  1:544669/1‑151 (MQ=255)                                                                                                            tctcGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTg                               >  1:512150/1‑151 (MQ=255)                                                                                                                   cctttAACCCGCTATCAGGATCATATAATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACa                        <  1:968917/148‑1 (MQ=255)                                                                                                                       tAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcg                    >  2:134190/1‑151 (MQ=255)                                                                                                                        aacccGCTATAAGAATAATATGAAAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAcc                     <  2:21686/146‑1 (MQ=255)                                                                                                                         aaCCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTATAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgcg                  >  2:1101909/1‑151 (MQ=255)                                                                                                                         aaCCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgcg                  >  1:340451/1‑151 (MQ=255)                                                                                                                            cGCTACCGGAATCATATAATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAcc               <  1:417276/151‑1 (MQ=255)                                                                                                                               tATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGc            >  1:606611/1‑151 (MQ=255)                                                                                                                                 tCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTc          >  1:1061071/1‑151 (MQ=255)                                                                                                                                   aGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCgg        >  1:890802/1‑151 (MQ=255)                                                                                                                                         atatGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTc      <  2:1018811/147‑1 (MQ=255)                                                                                                                                          tatGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtgt  >  2:1013048/1‑150 (MQ=255)                                                                                                                                                 aaCCCCCGCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtgt  <  2:80729/143‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                            TACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAACCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGT  >  NC_000913/1376359‑1376644

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑