Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,268,870	0	C	G	41.3%	81.0 / 12.8	47	L236V (CTG→GTG)	kdsA	3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase
Reads supporting (aligned to +/- strand):  ref base C (6/21);  new base G (19/0);  total (26/21)
Fisher's exact test for biased strand distribution p-value = 5.07e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAGT  >  NC_000913/1268730‑1269017                                                                                                                                             |                                                                                                                                                         aaGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCGCGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGa                                                                                                                                               <  1:285608/151‑1 (MQ=255)         ggTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGGCTGGCGGGGGCG‑GTTTTTTAAGCGCat‑c                                                                                                                                      >  2:979960/1‑151 (MQ=255)           tAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGGAGGCCTGGCGGGGGGG‑TTTTTTTaaaggcacc                                                                                                                                       >  2:115236/1‑142 (MQ=255)            accTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGTTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGTCGGGGCTG‑TTTATTGAAGCGCat‑ccg                                                                                                                                    <  1:815631/148‑1 (MQ=255)            aaCTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTGGGTCTGGGGGGGGTG‑GTTTTTTAAGGGCattc                                                                                                                                      >  1:955407/1‑147 (MQ=255)            aaCTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGGTG‑TTTTTTTAAACGCct‑ccgg                                                                                                                                   >  2:704863/1‑151 (MQ=255)             aCTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGGTG‑TTTTTTTAAGCGCat‑ccgg                                                                                                                                   >  2:378118/1‑150 (MQ=255)              cTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTTGGGGTTGCGGGGGCG‑GTTATTTAAggcgacccgg                                                                                                                                    >  1:352095/1‑140 (MQ=255)                   cGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGGGG‑TTTTTTTGAGGGCct‑cccggtccgg                                                                                                                             >  2:442811/1‑150 (MQ=255)                    ggTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGGTG‑TTTTTTTAAGCGCct‑ccggatccgg                                                                                                                             >  2:104106/1‑149 (MQ=255)                      tGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGGTG‑TTTTTTTAAGGGCat‑cccgatccgg                                                                                                                             >  2:911437/1‑147 (MQ=255)                        aTTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATg                                                                                                                       <  2:305739/151‑1 (MQ=255)                             cGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGaaa                                                                                                                  <  2:823609/151‑1 (MQ=255)                                   gACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGAt                                                                                                            <  1:943583/151‑1 (MQ=255)                                               ggaaggCCGCGTTCCGTTGGGCGCGGTTTCCGGTGGTCGGCGTGCTCAGGGGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCAGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATc                                                                                                    <  1:90208/142‑1 (MQ=255)                                                   tGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTGGGTCTGGCGGGGGTG‑TTTTTTTTAAGGCAT‑CCGGATCCGGGAAATGCGGAAAGGGATGGTCCCTCCGCGCTg                                                                                             >  1:976536/1‑150 (MQ=255)                                                   tGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGGTG‑TTTTTTTAAGGGCAT‑CCGGATCCGGGAAATGCGGAATGGGATGGTCCATcc                                                                                                   >  2:282207/1‑144 (MQ=255)                                                     ccGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCg                                                                                          <  2:103751/151‑1 (MQ=255)                                                          aTCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGc                                                                                    <  2:17744/151‑1 (MQ=255)                                                              gTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGGTG‑TTTTTTTAAAGGCAT‑CCGGATTCGGGAAATGCGGAAATTGGTGGGTCCTCCGCGCCGCCGCT‑GGC‑C‑aa                                                                               >  2:790491/1‑150 (MQ=255)                                                              gTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGGCTGGCGGGGGTG‑TTTTTTTGAACGCAT‑CCCGGTCCGGAACATGCGGAATGTGATGGGCCCTCCGCGCTGCCGCC‑GGC‑C‑aa                                                                               >  2:124107/1‑150 (MQ=255)                                                                    cgcAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGGAGGTCTGGCGGGGGTG‑TTTATTTAAGAGCAG‑CCGGATCCGGAACATGAGGAAAGGGTTTGGCCATCCGCGCCGGCGCC‑GGG‑T‑aaa                                                                              >  1:135761/1‑145 (MQ=255)                                                                     gcAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGGTG‑TTTATTGAAGCGCAT‑CCGGATCCGGGAAAAGCGAAAAGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTggga                                                                        >  2:585111/1‑148 (MQ=255)                                                                              ggtggtCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCa                                                              <  1:229817/151‑1 (MQ=255)                                                                                tggtCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTTAGTCTGGTGGGGATGTTTTATTGAAACGCA‑‑CCCCAGCCTGGACACGCGGAATGAGAATGTTCCTTCTCGCCGCCGCC‑GGC‑T‑AAACTTGAACCCTTCCTcta                                                             >  1:847596/1‑148 (MQ=255)                                                                                    cgtcgtGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGa                                                        <  2:175242/151‑1 (MQ=255)                                                                                     gtcgtGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTTTTTGAGCGCAT‑CCCGGTCCGGAAAATGCGGAAAGTGATGGGCCATCCGCGCCGCCGCT‑GGC‑T‑AAACTGGAAACGTTTCTCaa                                                             >  2:45815/1‑145 (MQ=255)                                                                                     gtcatagccaagTGGCTCAGCTGGCACGAGCAGGTATGCTGGTAGGTCTCGCGGAGCTG‑TTTATTCAAGCGAAG‑CCGGATCCGCAACATGCTAAATGTGTGGGGCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGACCCGTTCTTCAAg                                                            <  1:590698/135‑1 (MQ=255)                                                                                      tcgtGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGGCG‑TTTATTGAAAAGCATCCCGGAGCGGGAA‑ACGCGGAAAGTGGTGGTCCCTCCCGGCCGCCGCC‑GGC‑TAAAACGGGACCGGTTCCTCagc                                                            >  1:24569/1‑144 (MQ=255)                                                                                        gtGCTCGGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGaa                                                    <  1:469161/151‑1 (MQ=255)                                                                                        gtGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGa                                                     <  1:782018/150‑1 (MQ=255)                                                                                          gCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGaaa                                                   <  2:479260/150‑1 (MQ=255)                                                                                          gCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAg                                                  <  2:203411/151‑1 (MQ=255)                                                                                             cAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTCGGGCTGGCGGGGGTG‑TTTTTTTGAGCGCCT‑CCGGATGCGGGAAAAGCGGAAAGGGGTGGGCCATCCGCGCCGCCGCT‑GGG‑G‑AAACCGGAAACGtttc                                                                 >  1:774845/1‑131 (MQ=255)                                                                                             cAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGc                                                 <  2:812103/149‑1 (MQ=255)                                                                                              aGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTTGGGCTGGCGGGGGTG‑TTTTTTGTAGCGCAT‑CCGGGTCCCGGACAATGGAAAAGGGTTGGGCCCTCCCCGCTGCCCCTCGGT‑C‑AAACGGGAA‑CGTTCCTCCAGCAGATGaaa                                                   >  1:460770/1‑146 (MQ=255)                                                                                               ggTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGCGAtt                                             <  2:125849/151‑1 (MQ=255)                                                                                                                gAGGCGGTATGGCGGGAGGTCTGGCGGGGCTG‑TGTATGGAAGCGCAG‑CCGGATCGGGAACATGCGAAGTGTGAAGGGCCAACGGCGCTGCCGCT‑GGC‑T‑AGAATGGAACCGTTCCTCAAGCAGATGAAAGCGCTTGATGATgtggtg                                 <  1:117359/146‑1 (MQ=255)                                                                                                                   ccGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGCGATTGATGATCTGGTGAAAGGttt                         <  1:350219/151‑1 (MQ=255)                                                                                                                     ggTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGCGATTGATGATCTGGTGAAAGGTTTCg                       <  1:1035408/151‑1 (MQ=255)                                                                                                                       tATGGCGGTAGGTCTGGCGGGGGGT‑TTTTTTTAATCGCAT‑CCGGGTCCGGGACATTCGGGCTGTGGTGGTTCCTCCCCGCTAACCCT‑GGCTT‑AAACGGGAA‑CGGTCCTCAAGGAGATGAAAACGgatgatgattatggtagagggtt                         >  1:914492/1‑133 (MQ=255)                                                                                                                          ggCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGCGATTGATGATCTGGTGAAAGGTTTCgaaga                   >  2:503218/1‑150 (MQ=255)                                                                                                                             ggTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCCT‑CCGGATCCGGAACATGCGAAATGGGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTg               >  1:439812/1‑151 (MQ=255)                                                                                                                              gTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTgg              >  1:46562/1‑151 (MQ=255)                                                                                                                                         ggggCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCa     >  1:639087/1‑149 (MQ=255)                                                                                                                                         ggggCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAg   <  2:421461/151‑1 (MQ=255)                                                                                                                                          gggCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAGt  >  1:383530/1‑151 (MQ=255)                                                                                                                                             |                                                                                                                                                         AAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGCGGGGCTG‑TTTATTGAAGCGCAT‑CCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCT‑GGC‑T‑AAACTGGAACCGTTCCTCAAGCAGATGAAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAGT  >  NC_000913/1268730‑1269017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑