Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	48.1%	80.1 / 11.4	52	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (24/3);  new base C (0/25);  total (24/28)
Fisher's exact test for biased strand distribution p-value = 6.92e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCGG  >  NC_000913/1376356‑1376655                                                                                                                                                        |                                                                                                                                                       gCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAaca                                                                                                                                                        <  2:942239/150‑1 (MQ=255)      ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                                   <  1:167758/150‑1 (MQ=255)       cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                                   <  1:43026/149‑1 (MQ=255)       cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGc                                                                                                                                                 >  2:223850/1‑151 (MQ=255)         ccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCg                                                                                                                                               >  2:189114/1‑151 (MQ=255)         ccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCg                                                                                                                                               >  1:200727/1‑151 (MQ=255)          cgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGa                                                                                                                                              <  1:417126/151‑1 (MQ=255)           gATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGAt                                                                                                                                             >  2:285898/1‑151 (MQ=255)             tGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGc                                                                                                                                           >  1:549452/1‑151 (MQ=255)              gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGcc                                                                                                                                          >  2:858212/1‑151 (MQ=255)                         gTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTGACa                                                                                                                                >  1:435253/1‑150 (MQ=255)                             ccTGGCCGGCGACCGAAAAAGGGTGAGTGTTTCCCTGCGCGTACGGAAACGGGTCGCCGCGCGTCCCGGACCCGTGG‑TTTACCTCAAACCTTTAAC‑CCGCTATCAGAATCATATGACCAACCCCCCCGCCGATGCCCGCCGTTACAtcgt                                                                                                                            <  2:909975/150‑1 (MQ=255)                             ccTGGACGGCGACCGAAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGGACCCGTGG‑TGTATCTCGACCCGTAAAC‑CCGCTATCAGGATAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACAtcgt                                                                                                                            <  2:40799/150‑1 (MQ=255)                                gggcGGCGACCGAAAAATGGGGGGTGTTTCCCTGCGCGTACTGGAACGGGCCGCCGCGCGTACGGGACCGGTGG‑TTTATCTCGACCCTTAAAC‑CCGTTATCAGGATAATATGACAACCCCCCCCGCCGATGCCCGCCGTTACAtcgtcg                                                                                                                          <  1:318073/146‑1 (MQ=255)                                ggcgggCGCCCGAAAAGGGGTGAGTGATCCCCTGGGCTTATGGGAACAGGTCGCCGCGCGTCCCGAACCCGGGG‑TTTCTC‑CCAACCCTTAAACCCGTTATCAGGATAATATGAAAAACCCCCCCGCCGATCCCCGCCGTTACATCGTCGaa                                                                                                                        <  1:806386/147‑1 (MQ=255)                                   cGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAAc                                                                                                                     >  1:622426/1‑151 (MQ=255)                                    ggCGCCCGAAAAATGGTGGTTGATTCCCTGCGCTTCCGGGAAAGGGTCCCCGCGCGTCCCGAACCCGTGT‑TGTACCCCGACCCTTAAAC‑CCGTTATAAGGATAATAGGACAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAAc                                                                                                                     <  1:706475/150‑1 (MQ=255)                                     gCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGt                                                                                                                                    >  2:383224/1‑134 (MQ=255)                                     gCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACg                                                                                                                    >  1:868243/1‑150 (MQ=255)                                         ccaaaaaggggTGAGTTCTCCCCGGCGCGTACGGAAAGGGGTCCCCGCGCGCCCCGAAACGGGGG‑TTTATCCCAACCCTTTAAC‑CCCTTATCAGGATCATATGATCAACCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGAt                                                                                                                  <  2:340272/139‑1 (MQ=255)                                         ccGAAAAATGGTGGGTGATTCCCTGCGCGTACTGGAACAGGCCGCCGGCCGTACCGGAACCGGGG‑TTTATCCCAACCCTTTAAC‑CCTCTATCAGGTATATATGAAAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGa                                                                                                                   <  1:266959/147‑1 (MQ=255)                                            cAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTaa                                                                                                             >  2:494291/1‑150 (MQ=255)                                             aaagTGGTGAGTATTTCCCTGCGGTTACTGAACCAGGTCCCCGCGCGT‑CCGGGACCGGGGTTGTATCTC‑AACCTTTAAACCCGCTATCAGATTCATATAACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGAt                                                                                                                  <  1:903527/144‑1 (MQ=255)                                             aaaaTGGTGAGTGTTTCCCTGCGCGTACTGGAACAGTTCGCCGCGCGTCCCGGACCCGTGG‑TGTATCGCGAACCGTTAAC‑CCGCTATCGGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAAc                                                                                                           <  2:778949/151‑1 (MQ=255)                                             aaaaTGGTGAGTGATCCCCGGCGCGTCCGGAAACGGGTCGCCGCGCGTACCGGACCGGTGG‑TGTATCTCGACCTGTTAAC‑CCGCAATCAGGATCATATGACCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTa                                                                                                              <  2:895162/148‑1 (MQ=255)                                             aaaaGGGTGAGTGATTCCCTGCGCGTACTGAAACGGGGCGCCGCGCGTACGGGACCCGGGG‑TTTATCTCGACCCGTAAAC‑CCGTTATCAGGATCATATAATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTa                                                                                                              <  1:264785/148‑1 (MQ=255)                                                   gtgagtgaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                                     >  1:124432/1‑151 (MQ=255)                                                      agtgaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                                     >  1:256834/1‑148 (MQ=255)                                                         gttccccGGCGCGTACGGGAACGGGCCGCCGCGCGTCCCGGAACCGTGG‑TTTATCCCGAACCGTAAAC‑CCGCTATCAGGATAATATAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                                <  1:7821/146‑1 (MQ=255)                                                            ccccGGCGCTTACGGAAACAGCCCGCCGCGCGTCCCGGACCCGGGT‑TTTATCCCGACCCTTAAAC‑CCGTTACCGGGATAATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAg                                                                                                   <  1:221736/143‑1 (MQ=255)                                                              ccTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGc                                                                                          >  2:773940/1‑151 (MQ=255)                                                                 gcgcGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                                         >  1:943545/1‑149 (MQ=255)                                                                   gcttacggaaaCGGGCCGCCGCGCGTACGGGAACCGGGG‑TTTATCTCGACCCGTTAAC‑CCTTTACCAGGATCATATGATAACCCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGc                                                                                          <  1:466672/137‑1 (MQ=255)                                                                     gTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCt                                                                                   >  2:716671/1‑151 (MQ=255)                                                                          gtaaCGGGTCGCCGCGCGTACGGGACCCGTGG‑TGTCTCGCAACCCTTTAAC‑CCTCTATCAAGATAATTTGATCACCCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATca                                                                               <  1:922780/148‑1 (MQ=255)                                                                          ggAACAGGTCGCCGCGCGTACCGGACCCGTGG‑TGTATCTCGACCCTTTAAC‑CCGCTATCAGGATCATATGATAACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTa                                                                                  <  2:234865/147‑1 (MQ=255)                                                                              cAGGCCGCCGCGCTCCCCAAAACCGTGT‑TATATCTCGACCCTTTAAG‑CCGATACCAGGACAATATAAACAACCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATg                                                                           <  1:858195/150‑1 (MQ=255)                                                                               aGGTCGCCGCGGTTCCCGAAACTGTGG‑TTTCCCCCAACCCTTTAAC‑CCGCTATCAGGTTAAAAAAATCAACCCCCCCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAt                                                                                                 <  1:894593/127‑1 (MQ=255)                                                                                ggTCGCCGCGCGTCCCGAACCCGTGG‑TGTATCTCAAACCGTTAAC‑CCTCTATAAGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATg                                                                           <  2:724279/148‑1 (MQ=255)                                                                                ggTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACA‑CCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGagt                                                                        >  2:142940/1‑148 (MQ=255)                                                                                   cgccgcGAGTCCCGGAACGGTGG‑TTTGCCGGGAACCGTTAAG‑CCGTTACCGGGATAAAATGATCAACCCCCCCGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATc                                                                     <  2:711595/151‑1 (MQ=255)                                                                                    gccgcGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                                    >  2:828640/1‑151 (MQ=255)                                                                                     ccgcGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                                    >  2:244780/1‑150 (MQ=255)                                                                                       gcgcgTACGGGACCGGTGG‑TTTATCTCGAACCTTAAAC‑CCGCTATCAGGATAATATGAAAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATc                                                                     <  2:14330/147‑1 (MQ=255)                                                                                            tACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                                >  1:351014/1‑147 (MQ=255)                                                                                             aCCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGAt                                                            >  1:881207/1‑150 (MQ=255)                                                                                                ggAACCGGGG‑TGTATCTCG‑ACCGTTAAACCCGCTTTCGGGATCATTGGATCAACCCCCTCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGaagaag                                                              <  2:840883/145‑1 (MQ=255)                                                                                                  acccGTGG‑TTTATCCCCACCCGTAAAC‑CCGTTATAAGAATAAAATAAAAAACCCCCTCGCCGTTCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                                        <  1:127957/147‑1 (MQ=255)                                                                                                                  cGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCAt                                       >  1:520832/1‑151 (MQ=255)                                                                                                                            aacccGCTATCAGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcg                               <  2:408706/147‑1 (MQ=255)                                                                                                                                cgttataAGGTTAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAcc                          <  2:122855/148‑1 (MQ=255)                                                                                                                                  cTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTg                        >  2:28682/1‑151 (MQ=255)                                                                                                                                               atGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGc           >  1:81399/1‑151 (MQ=255)                                                                                                                                                       cacCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCg   >  2:556140/1‑151 (MQ=255)                                                                                                                                                        acCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCgg  >  2:436913/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                                                       GCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGG‑TGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCGG  >  NC_000913/1376356‑1376655

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑