Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,781,645	0	A	C	46.4%	77.4 / 12.2	56	V361G (GTT→GGT)	ypjA	adhesin‑like autotransporter
Reads supporting (aligned to +/- strand):  ref base A (24/6);  new base C (0/26);  total (24/32)
Fisher's exact test for biased strand distribution p-value = 1.54e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATATAATTGTTGTGTCAGCTTT‑CCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAACACATTGTCTG  >  NC_000913/2781499‑2781789                                                                                                                                                     |                                                                                                                                                 atatAATTGTTGTGTCAGCTTT‑CCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAAcccc                                                                                                                                              >  2:410112/1‑151 (MQ=255)    taATTGTTGTGTCAGCTTT‑CCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGcc                                                                                                                                           >  2:446775/1‑151 (MQ=255)         gttggGTCAGCTTT‑CCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTACTGCAACATCCATAACCCCGCCATTa                                                                                                                                       >  2:174448/1‑150 (MQ=255)                  gCTTTCCCCGCCGTTTTTGATTTTTTGCGTTCCGTTTTTGATATTGTTGCTTGTGGCTATGCCAAATTTATTAATATTCTGTGTCCCACCATTATTTATGTTTTTTGT‑CGCTTTCCCTCAAACACCCATACCCCCGCCATTATCTATTCgg                                                                                                                              <  1:461169/151‑1 (MQ=255)                          cgcctcTTTTGATTTTTGGCTTTCCGCTGTTGATATTGGTGCCTGTGGTTATGCCATAATTATTAATATTCTGTGTCCCACCATTAATTATGTTTTTTGT‑CGCTTTTCCTGCAACATCCATACCCCCGCCATTATCTATTCGGGTCGCATc                                                                                                                      <  2:394010/151‑1 (MQ=255)                          cgccgcTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATc                                                                                                                      >  2:829660/1‑151 (MQ=255)                              gtttttGATATTTTGCTTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGc                                                                                                                   <  2:825163/148‑1 (MQ=255)                              gcTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCt                                                                                                                  >  1:668476/1‑151 (MQ=255)                                ttttGATATTTTGCTTTCCGCTGTTGATTTGGGTGCTTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACAATTAATTATGGTATTTGT‑CGCTTTCCCTCCAACATCCAAACCCCCGCCATTATCTATTCGGGTCGCATCAGCt                                                                                                                  <  2:61420/149‑1 (MQ=255)                                        ttttGCTTCCCGCTTTTTTTTTTGGTGCTTGTGTTTATCCAATAATTATAAATATTCTGTGTGCCCCCATTAATTTTGGTTTTTGT‑CGCTTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTg                                                                                                         <  1:55282/150‑1 (MQ=255)                                        ttttGCGTTCCGCTTTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGTTATTTGT‑CGCGTTTCCTGCAACACCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCAtt                                                                                                          <  2:707561/149‑1 (MQ=255)                                           tGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGtt                                                                                                      >  2:23000/1‑150 (MQ=255)                                           tGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGtt                                                                                                      >  2:498407/1‑150 (MQ=255)                                            gCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTa                                                                                                     >  2:815202/1‑150 (MQ=255)                                                       ttGATTTTGGTGCTTGTGGTTTTGCCATAATTATTAATTTTCTGTGTGCCACCATTAATTATGTTTTTTGT‑CGCGTTTCCTGCAACATCAATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACAt                                                                                           <  1:672975/149‑1 (MQ=255)                                                          atatTGGTGCCTGTGGTTATGCCATAATTATTAATATTCTGTGTGCCCCCTTTAATTATGGTTTTTGT‑CGCTTTTCCTGAAACACCCAAACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTg                                                                                         <  2:354619/148‑1 (MQ=255)                                                           ttttGGTTCGTGTGGATATGCTAAAATTATAAATATTCTGTGTGCCACAATTAATTATGTTTTTTGT‑CGCGTTTCCTGCAACACCAATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTg                                                                                         <  1:770547/145‑1 (MQ=255)                                                               ggggcttgtgGCTATGCAATAATTATTAATTTTCTGTGTCCCACAATAAATTATGGTTTTTGT‑CGCTTTTCCTGCAACATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTa                                                                                 <  1:524598/145‑1 (MQ=255)                                                               ggTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCCCCATTAATTATGTTATTTGT‑CGCGTTTCCTGAAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTa                                                                                 <  1:474522/151‑1 (MQ=255)                                                                  gCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCt                                                                              >  2:383614/1‑151 (MQ=255)                                                                   ccTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCt                                                                              <  2:530771/150‑1 (MQ=255)                                                                     tgtgGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTAGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCTTTTATCttt                                                                            >  1:110002/1‑150 (MQ=255)                                                                      gtgGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTta                                                                           >  2:90823/1‑150 (MQ=255)                                                                      gtgGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTta                                                                           >  1:114530/1‑150 (MQ=255)                                                                       tgGCTATGCCATAATTATAAAAATTCTGGGTGCCACAATTAATTATGTTATTTGG‑CGCGTTTCCTCAAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCttt                                                                            <  1:797007/148‑1 (MQ=255)                                                                        ggttATCCCAAAATTTTAAATATTCTGTGTCCCACCTTTAATTGTGGTTTTTTT‑CGCTTTCCCGGAAACATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTta                                                                           <  1:287121/145‑1 (MQ=255)                                                                         gttgtGCCATAATTTTTAATTTTCTTTTGCCCACCATTAATTATGGTTTTGGT‑GGTGTTTCCTGCAACACCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTtaa                                                                          <  1:792659/144‑1 (MQ=255)                                                                          cTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTaataat                                                                      >  1:843097/1‑151 (MQ=255)                                                                           tagccaaTAATTTTTAATTTTCTGTGTCCCACCTTTAATTATGTTTTTTGT‑CGCTTTTCCTGAACCTTCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTtaataa                                                                       <  2:796309/143‑1 (MQ=255)                                                                              gCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTc                                                                  >  1:566613/1‑151 (MQ=255)                                                                                 atatTTATAAATTGTCTTTGTCCCCCCATTAATTTTGGTTTTTGT‑CGCTTTTCCGGCAACACCAATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGt                                                                   <  1:174877/147‑1 (MQ=255)                                                                                  tAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGt                                                              >  2:853134/1‑151 (MQ=255)                                                                                       attaCTATTCTGTGAGCCACCATTATTTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCCCCATTATCTATTCGGTTCGCATCAGGTTTATCATTGTTTAAAACTGACATCTTTCCTTTATCTTTAATAATCGACTTGTTTGcc                                                         >  1:491126/1‑151 (MQ=255)                                                                                           atatTCTGGGGGCCACGATAAATTTTGTAATTTTG‑CGTTTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAAc                                                     <  2:547274/151‑1 (MQ=255)                                                                                            tatTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAAcc                                                    >  1:399122/1‑151 (MQ=255)                                                                                              ttCTGTGTCCCCCCATTAATTATGGTTTTTGT‑CGCGTTTCCTGCAACATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAAcc                                                    <  1:511001/149‑1 (MQ=255)                                                                                              ttCTGTGTCCCACCATTATTTTTGTTTTTTTC‑CGCTTTTCCTGCAACATCAATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGa                                                       <  1:573621/146‑1 (MQ=255)                                                                                                 tgtgtgCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATg                                               >  1:548610/1‑151 (MQ=255)                                                                                                  gtgtgCCACCATTAATTATGGTTTTTGT‑CGCTTTTCCTGCAACACCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCatat                                                <  2:583838/149‑1 (MQ=255)                                                                                                   tgtgCCACTATTAA‑TGTTGTATTTTTGCGTTTTTCCTACACCCCCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTCTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGATCCat                                                  <  1:449622/146‑1 (MQ=255)                                                                                                   tgtcCCACAATTAATTATGTTATTTGT‑GGTTTTTCCTGAAACATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCata                                                 <  1:764914/147‑1 (MQ=255)                                                                                                       cccccaTTAATTATGTTTTTTGT‑CGCTTTTCCTCAAACACCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCat                                                  <  1:341243/139‑1 (MQ=255)                                                                                                          ccaTTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGt                                      >  1:766837/1‑151 (MQ=255)                                                                                                          ccaTAATTTATGTTTTTTGT‑CGTTTTTCCTGCAACATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTAt                                        <  1:517958/149‑1 (MQ=255)                                                                                                             ttaattaTGTTATTTGT‑CGCTTTTCCTGCAACATCAATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCt                                    <  1:280378/150‑1 (MQ=255)                                                                                                             ttaattaTGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCt                                    >  1:805568/1‑150 (MQ=255)                                                                                                               aattaTGTTATTTGT‑CGCTTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTa                                   <  2:96541/149‑1 (MQ=255)                                                                                                               aattaTGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTaa                                  >  2:236536/1‑150 (MQ=255)                                                                                                               aattaTGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTaa                                  >  1:784692/1‑150 (MQ=255)                                                                                                                 ttgtGGTATTTGT‑GGTTTTTCCTGCAACATCCAAACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAAt                                <  1:528138/147‑1 (MQ=255)                                                                                                                        aTTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCg                        >  2:150148/1‑151 (MQ=255)                                                                                                                         tttGT‑CGTGTTTCCTGCACCATCCATACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGaccacc                         <  2:298840/149‑1 (MQ=255)                                                                                                                                 cgTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTcc                  >  2:726201/1‑149 (MQ=255)                                                                                                                                      ccTGCAACACCCAAACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAaca           <  2:466596/151‑1 (MQ=255)                                                                                                                                                caaTACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAACACATTGTCTg  <  2:668518/148‑1 (MQ=255)                                                                                                                                                 aaTACCCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAACACATTGTCTg  <  2:446818/148‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                 ATATAATTGTTGTGTCAGCTTT‑CCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGTGTGCCACCATTAATTATGGTATTTGT‑CGCGTTTCCTGCAACATCCATAACCCCGCCATTATCTATTCGGGTCGCATCAGCTTTAGCATTGGTTAAAACTGACATTGTTCCTTTATCTTTAATAATCGTCTTGTTTGCCGAACCATATGCGTTTATGTCTAAATGACCACCGTTTTCCAGCAACACATTGTCTG  >  NC_000913/2781499‑2781789

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑