Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,248,437	0	A	C	44.4%	87.5 / 10.5	54	G32G (GGT→GGG)	lysP	lysine transporter
Reads supporting (aligned to +/- strand):  ref base A (24/6);  new base C (0/24);  total (24/30)
Fisher's exact test for biased strand distribution p-value = 5.09e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGACGATTGG  >  NC_000913/2248289‑2248584                                                                                                                                                       |                                                                                                                                                     aCGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTAcc                                                                                                                                                    <  1:832315/151‑1 (MQ=255)  cGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCg                                                                                                                                                   >  2:433734/1‑151 (MQ=255)    aaCCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAt                                                                                                                                                 >  1:921545/1‑151 (MQ=255)       cGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGa                                                                                                                                             <  2:945008/151‑1 (MQ=255)                       tGCAGCCAGTACACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAatc                                                                                                                             >  1:845779/1‑151 (MQ=255)                            caagtccccggagaCTGGTCATCAGGAAAAAACCCACCGGGCAAATCAGCATAAGGGAGAGCAACCCCCCCCCGGGACCTGCATGAAAAA‑TGGTGGCGCCAGAGGCAAAAAAAAGACT‑TGTCCCGAT‑GAAACCGCCAATGGCAATCATCg                                                                                                                         <  2:572035/140‑1 (MQ=255)                                ttCACCGAGACTGGTCATAAGGAAGTAAACCATAAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGt                                                                                                                        >  2:340909/1‑147 (MQ=255)                                 cccccGAGACTGGTCAGCAGGAAAAAACCCACCAGGCCAATCACAATATACGAGAGCAATCCCCCCCCCGGCCCTGCCTGAAAAA‑TCGTTGCGCCAGAGGAAAAAAAAACCCC‑TCTCCCGAG‑GAACCCGCCAATGGCAATCATCGTCAg                                                                                                                     <  2:461782/146‑1 (MQ=255)                                     cGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGAcg                                                                                                               >  2:1775/1‑151 (MQ=255)                                      gagaCTGGTCATCAGAAAGAAACCCATCAGCCAAATCAGCATATACGAGAGCAATGCCCCGCCCGGCCCTGCCTGAGAAA‑TCGTTGCGCAAGAGGAAAAAAAAAGCCC‑TGTCCCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGAcg                                                                                                               <  1:332622/150‑1 (MQ=255)                                       agaCTGGTCATCAGGAAGCAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGAcgc                                                                                                              >  2:1013361/1‑150 (MQ=255)                                            ggTCACAAGAAAGTAACCCACCAGCACAATCAGAAAATACGAGAGAAACCCCCCCCCCGGCCCTGCCGGAAAAA‑TCGTGGCGCCGGAGGCAAAAAAAAGCCC‑TGTCCCGAT‑GAAACCGCCAATGGCAATCATCGTCAGGTGACgcgc                                                                                                            <  2:108314/147‑1 (MQ=255)                                                agaagaaataaaaCCACCAGGCCAATCAGCATAAAGGAGACCACCCCCCCCCCCGGCCCTCCATGAGAAT‑TCGTTGCCCAAGAGACAACAAAAAGCCT‑TGTCCCGAG‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTaa                                                                                                      <  1:285820/139‑1 (MQ=255)                                                  caGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTc                                                                                                   >  1:1009596/1‑150 (MQ=255)                                                      aaGTAACCCACCAGCCAAATCAGAAAATAGGAGAGAAATCCCCCCCCCGGCCCGGCCGGAAAAA‑GCGTTGCGCCAGGGGAAAAAAAAAGCCC‑TGTCCCGAT‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCa                                                                                                  <  1:557654/147‑1 (MQ=255)                                                               aTCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGccc                                                                                      >  1:222794/1‑150 (MQ=255)                                                               aTCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCg                                                                                     >  1:461493/1‑151 (MQ=255)                                                                  aGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGgcg                                                                                  >  1:634279/1‑151 (MQ=255)                                                                     ccAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCtt                                                                               >  2:710805/1‑151 (MQ=255)                                                                           atcaaaaaggacagCAATGCCCCCCCCGG‑CCTCGCGGAAAAACCCGTTGCGCGGGGGGCAAAAAAACACCC‑TCTCCCAAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTgg                                                                         <  1:561802/139‑1 (MQ=255)                                                                               tataCGAGAGAAATCCCCCGCCCGGCCCTGCCTGAAAAA‑TCGTTGCGCCAGAGGCAAAAAAAAGCCC‑TGTCCCGAT‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGt                                                                        <  1:340877/148‑1 (MQ=255)                                                                                   cGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGtt                                                                 >  1:783095/1‑151 (MQ=255)                                                                                    gagaCCAACCCCCCGCCCGGCCCTGCCTGAAAAA‑TCGTTGCGCCAGAGGCAAAAAAAAGCCC‑TGTCCCGAT‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGttt                                                                <  1:385512/151‑1 (MQ=255)                                                                                      gagCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCg                                                              >  1:359152/1‑151 (MQ=255)                                                                                         cAACGCCCCGCCCGGCCCTGCCTGAAAAA‑CCGTGGCCCCAGAGCAAAAAAAACGCCC‑TTTCCGGAT‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGa                                                            <  1:450369/150‑1 (MQ=255)                                                                                          actcccccGCCCGGACCGGCCTGAAAAA‑TCGTGGCGCCAGAGCCAAAAAAAAGCCC‑TGTCCCGAG‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGtt                                                                 <  1:865098/140‑1 (MQ=255)                                                                                          actGCCCCCCCCGTCCCTGCGTAAGAAA‑CCGTGGCACCAGGGGAAACAAAAACACC‑AGCCCCGAC‑GTAGCCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCgg                                                             <  1:421495/146‑1 (MQ=255)                                                                                          aaTGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGaa                                                           >  1:91640/1‑150 (MQ=255)                                                                                           aTGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAAc                                                         >  1:92149/1‑151 (MQ=255)                                                                                            tGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAAcc                                                        >  2:979075/1‑151 (MQ=255)                                                                                              ccccccccGGCCCTCCCTGAAAAC‑CCGTTCCCCGAAAGCCAAAAAAAACCCC‑T‑TCCCCATGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGaaa                                                          <  1:523914/147‑1 (MQ=255)                                                                                              ccccGCCGGGACCCGCTGAAAAAA‑TGGTTGGGCAAGGCGCAAAAAAAAGCCC‑TGTCCCGAG‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCAt                                                      <  1:209415/151‑1 (MQ=255)                                                                                                 cccccgccccggcatgAAAAA‑TCTTGGCGCCAGGGACAAAAAAAAGCCC‑TGTACCGAG‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACa                                                   <  2:534660/137‑1 (MQ=255)                                                                                                   cccgGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACaa                                                  >  1:543201/1‑150 (MQ=255)                                                                                                    ccgGCCCTCCCTAAAAAA‑TCGTGGCGCCAGAGGAAAAAAAAAGCCC‑TGTCCCGAG‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACaaaa                                                <  2:714485/151‑1 (MQ=255)                                                                                                     cgGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACaaaa                                                >  2:520972/1‑150 (MQ=255)                                                                                                       gACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATg                                             >  1:726355/1‑151 (MQ=255)                                                                                                        aCCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGc                                            >  1:843018/1‑151 (MQ=255)                                                                                                             ccggaaaaa‑CCGTGGCGCAAGAGAAAAAAAAAAGCCT‑TGTCCGGAG‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATcc                                       <  2:558647/145‑1 (MQ=255)                                                                                                                 agaAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCt                                   >  1:836998/1‑151 (MQ=255)                                                                                                                   aaa‑TCGTGGCGCCAGAGGCAAAAAAAAGCCC‑TGCCCCGAT‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCtt                                  <  2:82501/150‑1 (MQ=255)                                                                                                                    aa‑TCTTGGCGCCAGAGCAAAAAAAAAGCCC‑TGTCCCGAT‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACAATACAAAAATGCTATCCATCTTaa                                <  1:792445/151‑1 (MQ=255)                                                                                                                    aa‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTa                                 >  1:324291/1‑150 (MQ=255)                                                                                                                          tcgcgcGAGAGGAAACAAAAAGACC‑TGTCCCGAG‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAAt                            <  1:557493/148‑1 (MQ=255)                                                                                                                               ccAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGgcg                      >  2:952442/1‑151 (MQ=255)                                                                                                                                 agagGAAAAAAAAAGCCC‑TGAACGGAG‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAgg                        <  2:92853/147‑1 (MQ=255)                                                                                                                                   gggCAAAAAAAAGGCCTTGCCCGGAA‑GGACCCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGgc                       <  1:855776/146‑1 (MQ=255)                                                                                                                                    ggCAAAAAAAAGCCC‑TGTCCCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAAGGAg                         <  1:454530/143‑1 (MQ=255)                                                                                                                                    ggCAAAAAAAAGCCC‑TGTCCCGAG‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGa                   <  1:891022/149‑1 (MQ=255)                                                                                                                                       aaaaaaaaGCCC‑TGTACCGAG‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGt               <  1:474426/147‑1 (MQ=255)                                                                                                                                             aaGCCC‑TGTCCCGAG‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGAc        <  1:659333/151‑1 (MQ=255)                                                                                                                                             aaGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGAc        >  1:408715/1‑151 (MQ=255)                                                                                                                                                 cc‑TGTCCCGAT‑GAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGACGAtt    <  2:945100/151‑1 (MQ=255)                                                                                                                                                     gTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGACGATTgg  <  1:433738/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                     ACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAA‑TCGTTGCGCCAGAGGCAACAAAAAGACC‑TGTACCGAT‑GGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGACGATTGG  >  NC_000913/2248289‑2248584

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑