Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,578,143	0	A	C	43.4%	78.0 / 24.2	53	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
Reads supporting (aligned to +/- strand):  ref base A (25/5);  new base C (0/23);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 2.61e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTCGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATC  >  NC_000913/2577996‑2578278                                                                                                                                                     |                                                                                                                                        gttCGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAAccc                                                                                                                                      <  1:19505/151‑1 (MQ=255)  ttCGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAAcccc                                                                                                                                     >  1:33331/1‑151 (MQ=255)    cGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCa                                                                                                                                    <  1:22078/150‑1 (MQ=255)              gACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGt                                                                                                                          >  2:609776/1‑150 (MQ=255)                cAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTAcc                                                                                                                       >  1:233628/1‑151 (MQ=255)                 aaCTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCg                                                                                                                      >  1:41818/1‑151 (MQ=255)                  aCTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGt                                                                                                                     >  2:621320/1‑151 (MQ=255)                         tAAATTTGTCCGGGTCGAGCTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGAACCGTTag                                                                                                                  >  2:177094/1‑147 (MQ=255)                                  cggggTCGATTTCGTAACCTTCAATGTAAAATACATCAACCCCGGCAATTTTCTAAAACAGACCGCCTTTCCCTCCCATCACGGTTTTGCC‑TGCCGGCGCCCAATTTTTGCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGcc                                                                                                       <  1:422674/147‑1 (MQ=255)                                  ccGGGTGGAGTTCTACAACTCAAATTCAAAATACACAACCCCCGGCGAATTTCTAAAACAGAACGCCCTTGCCTCCCACCACCGGTTTGCC‑TGCCAGCGCCCCATTGTGGCCTAACCCCAACACCGCCGTACCGTTAGAGATCACCGc                                                                                                        <  2:772472/148‑1 (MQ=255)                                             cggTCACCTTCAATGCAAAATCCACCACCCCCGGCGATTTTCTAAAACAGACCCCCCTT‑CCCTCCCTCCCCGGTTTGCCGTCCCGGCGCCCCACGGTTGCCACCCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTc                                                                                          <  2:92509/149‑1 (MQ=255)                                              cGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCg                                                                                         >  2:50956/1‑151 (MQ=255)                                               gTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCgg                                                                                        >  1:152117/1‑151 (MQ=255)                                               gTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCgg                                                                                        >  2:89619/1‑151 (MQ=255)                                                  atcTTAAATGTAAAATACATCAACCCCGGCAATTTTCTTAAACAGACCGCCCTTCCCTTCCACCCCCGTTTTGCC‑TGCCAGCGCGCAAATGTTGCCTACCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGc                                                                                      <  1:673049/148‑1 (MQ=255)                                                  accTTCAATGTCAAATACACCAATCCCGGCAAATTTCTAAAACAGAACGCCCTTGCCTCCCATCCCCGGTTTGCC‑TGCCAGCGCGCCAATTTTCCCTACCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCg                                                                                         <  1:745693/145‑1 (MQ=255)                                                    cTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGt                                                                                   >  2:111376/1‑151 (MQ=255)                                                     ttCAATGACAAATACATCACCCCCGGCGATTTTCTAAAACAGACCCCCCTTGCCTCCCACCCCCGTTTTGCC‑TGCCAGCGCGCCAATTTTGCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCg                                                                                     <  2:784295/148‑1 (MQ=255)                                                     ttCAATATAAAATACATCAACCCCGGCAATTTTCTTAAACAGACCGCCCTTCCCTCCCCCCCCCGTTTTCCC‑GCCCAGCCCCCCATTTTTGCCAACCCCCACCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGt                                                                                   <  2:634357/150‑1 (MQ=255)                                                      tCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGtat                                                                                 >  2:315619/1‑151 (MQ=255)                                                        aaTTTCAAATCCACCAACCCGCGCGATTTTAAAAAACAAACCCCCCTTCCCTTCCACCCCCGGTTGTCC‑TCCCAGCGCCCCATTTTTCCCCACCCCCAGCGCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGta                                                                                  <  2:20540/148‑1 (MQ=255)                                                        aaTGTAAAATACATCATCCCCGGCGATTTTTTAAAACAGAACGCCCTTGCTTCCCACCACCGTTTGGCT‑GGCCAGCGCCCCAATGTTGCCAAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGtata                                                                                <  2:659370/150‑1 (MQ=255)                                                        aaTGTAAAATACATCACCCCCGGCAATTTTCTAAAACAGACCCCCCTTCCCTCCCACCCCCGGTTTCCC‑TCCCGGCGCCCCAATGTTCCCAACCCCCACCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTatat                                                                               <  2:168725/151‑1 (MQ=255)                                                        aaTGTAAAATACATCAACCCCGGCAATTTTCTAAAAAAGACCCCCCTTCCCTCCCACCCCCGTTTTGCC‑TGCCAGCGCGCCAATGTTGCTAACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGta                                                                                  <  1:874683/148‑1 (MQ=255)                                                         aggTCAAATACATCAACCCGGGCAATTTTCTAAAACAGACCGCCCTTCCCTCCCACCCCCGTTTTGCC‑GGCCAGCGCGCAAATGTGGCCAACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATAtt                                                                              <  1:671550/149‑1 (MQ=255)                                                            tCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGt                                                                           >  2:331078/1‑151 (MQ=255)                                                                   cATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCttt                                                                    >  1:334648/1‑151 (MQ=255)                                                                       aaccccGGCGAATTTCTTAAACAGACCGCCCTTGCCTCCCATCCCGGGTTGGCC‑TGCCAGCGCCCAAATGTTCCCTACCCCCACCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTa                                                                  <  1:35308/146‑1 (MQ=255)                                                                         tCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACTGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACgg                                                              >  1:291933/1‑151 (MQ=255)                                                                           ccGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGt                                                            >  2:831469/1‑151 (MQ=255)                                                                           ccGGCGAATTTCTAAAACAGAACCCCCTTCCTTTCCATCCCCGGTTTGCC‑TGCCGGCGCGCAAGTGTTGCCCACCCCCACCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTaa                                                                 <  1:699124/146‑1 (MQ=255)                                                                                   tttCTTAAACAGACCCCCCTTCCCTCCCATCCCCGGTTTGCC‑GGCCAGCGCGCCAATGTTGCCTACCTCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTc                                                     <  1:316842/150‑1 (MQ=255)                                                                                   tttCTAAAACAGACCCCCCTTGCCTCCCACCCCCGTTTTGCC‑TGCCAGCGCGCAAATGTTCCCAACCCCCACCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTc                                                     <  1:887008/150‑1 (MQ=255)                                                                                    ttCTAAAACAAACCGCCCTTCCCTCCCACCCCCGTTTGCCC‑TCCCGGCGCCCAAATTTGCCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCg                                                    <  2:465280/150‑1 (MQ=255)                                                                                      cTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGAtt                                                 >  1:74429/1‑151 (MQ=255)                                                                                         aaaaAGACCCCCCTTCCCTCCCACCACCGTTTTCCC‑TGCCAGCCCCCAAATTTTCCCAACCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTc                                               <  1:836175/150‑1 (MQ=255)                                                                                         aaaCAGAACCCCTTTCCCTCCCACCCCCGTTTTGCC‑TGCAAGCGCCCAAATTTTCCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGa                                                   <  1:932980/146‑1 (MQ=255)                                                                                          aaCAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCa                                              >  1:774501/1‑150 (MQ=255)                                                                                               accGCCCTTGCCTTCCACCCCCGGTTTGCC‑TGCCAGCGCGCAAATGTTGCCAAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGAc                                          <  1:855310/147‑1 (MQ=255)                                                                                                 cGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGATAAgg                                      >  1:825490/1‑151 (MQ=255)                                                                                                 cGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAgg                                      >  2:215422/1‑151 (MQ=255)                                                                                                  gCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGt                                     >  1:204548/1‑151 (MQ=255)                                                                                                  gCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGt                                     >  1:432729/1‑151 (MQ=255)                                                                                                         ccttccttCTCCTGTTTCCC‑CCCAGGCGCCCTATTGTTGCTTACCCCCAGCTCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCaa                              <  2:715444/151‑1 (MQ=255)                                                                                                         cctcccaccccgggTTTGCC‑TGCCGGCGCGCAATTGTTGCCTACCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCaa                              <  2:715208/139‑1 (MQ=255)                                                                                                          cTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAAc                             >  1:345015/1‑151 (MQ=255)                                                                                                           tcccgccACCGTTTTGCG‑TGCCAGCGCCCAAGTGTCGCCTACCCCAAGAACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACaa                                        <  1:781950/133‑1 (MQ=255)                                                                                                                   ccGGTTTGCC‑TGCCAGCGCGCCAATTTTGCCAACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTg                        <  2:831506/147‑1 (MQ=255)                                                                                                                         ttcccggccAGCGCCCAAATGTTCCCTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAg                   <  2:150609/141‑1 (MQ=255)                                                                                                                            c‑tgccAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGcc             >  2:907252/1‑149 (MQ=255)                                                                                                                                 cAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGcc       >  1:855746/1‑151 (MQ=255)                                                                                                                                       gcCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGcc       >  1:608358/1‑145 (MQ=255)                                                                                                                                        ccagtttccccTACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATc  <  2:888191/140‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                        GTTCGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCC‑TGCCAGCGCGCCAATGTTGCCTAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATC  >  NC_000913/2577996‑2578278

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: ‑