Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,435,725	0	C	A	40.4%	90.5 / 22.5	53	intergenic (‑106/+35)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
Reads supporting (aligned to +/- strand):  ref base C (29/2);  new base A (0/21);  total (29/24)
Fisher's exact test for biased strand distribution p-value = 1.32e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGAC  >  NC_000913/1435586‑1435874                                                                                                                                              |                                                                                                                                                      aaaTATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGccc                                                                                                                                            >  2:510824/1‑151 (MQ=255) aaaTATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGccc                                                                                                                                            >  2:22292/1‑151 (MQ=255)        gATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATa                                                                                                                                      >  2:577917/1‑150 (MQ=255)           aGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAAc                                                                                                                                    >  2:728882/1‑149 (MQ=255)                aaaGAATCTTTCTGTTAAAAAACCCTCTTTTTTTAGTACCCGAAAAAAGTGTAACCCCAGATGACATTTTTTGTGAAATGAGGGAGTCCACTTTTTTAATTAAGACAAAA‑GGAGG‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGc                                                                                                                             <  2:493978/150‑1 (MQ=255)                  aaaaTCTTTTTATTCAAAAAACCCTCTTTTTTTGTCTCTGTATAAGGTGTACCGCAAGATGACCATTTTTGTATAACGGCGATGTCCATTTTTTTAATAAATACCAAA‑GAAGA‑AAAAAAAAACAAAAAAGTCCCGCCATAACAGCGGGCag                                                                                                                           <  2:69607/149‑1 (MQ=255)                    aaTCTTTTTTTTCAAAAACCCTCTTTTTTTAGTACCCGCAAAAAGTATAACCCCAGATGACTTTTTTTGTGAAATGAGGGAGTTCACTTTTTTAATTTAGAAAAAA‑GGAGA‑AAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCagga                                                                                                                         <  2:14631/151‑1 (MQ=255)                    aaTCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGT‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCagg                                                                                                                          >  1:592410/1‑150 (MQ=255)                         tttttttaaTAAACCCTCCTTTTTTAGTACCCGAAAAAATTGTAACACCAGATGACATTTTTTGTAAAATGCCGGATTTCCTTTTTTTAATTAAGAAAAAA‑GGAGG‑AAGAATAAGAAAAAAAAGCCCGCCATAACAGCGGGCAggagga                                                                                                                      <  2:421423/141‑1 (MQ=255)                         ttCTTTTAAAAAACCCTCTTTTTTTAGTACCCGAATAAAGTGTACCGCAAGATGACTTTTTTTGTAAAATGAGGGAGTTCACATTTTTATTTAAGAAAAAA‑GGAGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCaggagg                                                                                                                       <  1:231445/148‑1 (MQ=255)                         ttCTGTTAATAAACCCTCCTTTTTAAGTATCCAAATAAAGTGTAGCGCGAAATGCCTTTTTTTGTTTAATGA‑GGGGTTCCAATTTTTAATTTTAAAAAAA‑GGGGGAAAGAAAAAGAAAAAAAGGCCCGCCATAACAGCGGGCAggagga                                                                                                                      <  1:984349/149‑1 (MQ=255)                          ttggTTCAAAAACCCCCTTTTTTTTGTCTCCTCAAAAAGTGTCACACAGGAAAACATTTTTTGTTAAAGGACGGTTTTCACTTTTTTATTTTAGATAAAG‑GGAGA‑AAAAATACGAAAAAAACGCCCGCCATAACAGCGGGCAGGAGGAtt                                                                                                                    <  2:168319/147‑1 (MQ=255)                                 aTAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTg                                                                                                            >  2:200323/1‑151 (MQ=255)                                      aCCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATaa                                                                                                        >  2:135626/1‑150 (MQ=255)                                         tcctGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAAcc                                                                                                     >  2:955031/1‑150 (MQ=255)                                         tcctGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAAcc                                                                                                     >  2:477095/1‑150 (MQ=255)                                            tGTTTTAGTACCCAAATAAAGTGTACCCCCAGATGACTTTTTTTGTGAAAGGAGGGATTTCATTTTTTTAATTAAGAAAAAA‑GGAGG‑AAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCa                                                                                                    <  2:529571/148‑1 (MQ=255)                                                  agtacccaaaaaaaGTGAAACGCCAAATGACATTTTTTGTGAAAGGAGGGAATTCACATTTTTAATTTAAAAAAAA‑GAAGA‑AAAAAAAAAAAAAAAACCCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAg                                                                                           <  2:800679/140‑1 (MQ=255)                                                         gCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAat                                                                                    >  1:154343/1‑151 (MQ=255)                                                           aaaaaGTGAAACCCCAGATGACTTTTTTTGTGAAAGGACGGAGTTCACTTTTTAAATTTAGAAAAAA‑GGAGA‑AAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAat                                                                                    <  2:387466/147‑1 (MQ=255)                                                           aTAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAatat                                                                                  >  1:131890/1‑151 (MQ=255)                                                           aTAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAatat                                                                                  >  2:1000070/1‑151 (MQ=255)                                                             aaaGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATatc                                                                                 >  1:190408/1‑150 (MQ=255)                                                                    aaCGCGAAATGACTTTTTTTGTTAAATGGGGGAATTCAC‑TTTTATATTTAAAACAAAGGGAGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTag                                                                         <  2:807315/151‑1 (MQ=255)                                                                    aaCGCCAGATGACTCTTTTTGTGTAATGACGGAGTCCACATTTTTAATTAAGACAAAA‑GGAGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCgg                                                                            <  2:766147/148‑1 (MQ=255)                                                                        ccAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTag                                                                         >  1:338496/1‑147 (MQ=255)                                                                         cAGATAACATTTTTTGTGAAAGGACGGAGTTCACATTTTTAATTAAAAAAAAA‑GGAGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAgaga                                                                      <  1:851685/149‑1 (MQ=255)                                                                            aTGCCATTTTTTGTGAAATGACGGAGTTCACATTTTTAATTTAGACAAAG‑GGAGA‑AAGAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATg                                                                    <  1:121658/148‑1 (MQ=255)                                                                              gactttttttGTGTAATGACGGAGTTCACATTTTTAATTAAGATCAAA‑GGAGG‑AAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGcc                                                                  <  1:511875/143‑1 (MQ=255)                                                                                 acTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGc                                                            >  2:695445/1‑151 (MQ=255)                                                                                   tttttGTTAAAGGACGAATTACAATTTTTTAATTAAAAAAAAA‑GAAGG‑AAAAAAAAGAAAAAAACCCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGAt                                                                     <  2:76774/140‑1 (MQ=255)                                                                                   tttttGTGTAATGACGGAGTTCACATTTTTAATTAAGAAAAAA‑GGAGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCa                                                           <  2:218859/150‑1 (MQ=255)                                                                                     tttGTGTAATGAGGGATTTCACATTTTTAATTTAGATAAAA‑GGAGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGc                                                         <  1:901161/150‑1 (MQ=255)                                                                                             aTGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCt                                                >  1:582701/1‑151 (MQ=255)                                                                                                aCGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTc                                             >  1:207829/1‑151 (MQ=255)                                                                                                  ggAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCGGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCAt                                           >  1:133598/1‑151 (MQ=255)                                                                                                  ggAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCAt                                           >  2:82232/1‑151 (MQ=255)                                                                                                     gTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCtt                                        >  1:697338/1‑151 (MQ=255)                                                                                                      ttCATATTTTTAATTAAGATCAAA‑GGAGA‑AAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATc                                          <  1:510835/148‑1 (MQ=255)                                                                                                        caattttttAATTAAGAAAAAA‑GGAGG‑AAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCtt                                        <  2:52235/144‑1 (MQ=255)                                                                                                            tttttAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCa                                  >  1:536227/1‑150 (MQ=255)                                                                                                            tttttAATTAAGAAAAAG‑GGAGA‑AAAAAAAAGCAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTc                                       <  1:850937/145‑1 (MQ=255)                                                                                                               ttAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAAc                                >  1:252900/1‑149 (MQ=255)                                                                                                                      agaaaaaa‑GGAGA‑AAGAATAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGAtt                       <  1:89424/146‑1 (MQ=255)                                                                                                                         tCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGAtttt                     >  1:296127/1‑150 (MQ=255)                                                                                                                            aa‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTtat                   >  1:125028/1‑149 (MQ=255)                                                                                                                                gaga‑aAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCa              <  1:315482/151‑1 (MQ=255)                                                                                                                                 agg‑aAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCa              >  1:14523/1‑150 (MQ=255)                                                                                                                                 agg‑aAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCa              >  1:527041/1‑150 (MQ=255)                                                                                                                                   gtaagaaTAAGGAAAAAAGGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCaa             <  2:388985/148‑1 (MQ=255)                                                                                                                                     aagaaTAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGt          >  2:947484/1‑151 (MQ=255)                                                                                                                                           aaGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTgg    >  2:664792/1‑151 (MQ=255)                                                                                                                                            aGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTgg    >  2:196000/1‑150 (MQ=255)                                                                                                                                              cAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGAc  >  1:930868/1‑150 (MQ=255)                                                                                                                                              |                                                                                                                                                      AAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAA‑GGAGG‑AAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGAC  >  NC_000913/1435586‑1435874

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑