Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_pae_pgi	2,263,081	G→A	8.6%	L139L (CTG→TTG)	fruB ←	fused fructose‑specific PTS enzymes: IIA component/HPr component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_pgi	2,263,081	0	G	A	8.6%	125.4 / 4.0	50	L139L (CTG→TTG)	fruB	fused fructose‑specific PTS enzymes: IIA component/HPr component
Reads supporting (aligned to +/- strand):  ref base G (17/26);  new base A (2/2);  total (21/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.47e-01

TTGGTGACGAAAGTGGCGTCAACTGCCCCCGCCTCTTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGCCCAGATGTTCATCCGAGCTGGCAGCAATACCGATTGCCACGTACGCTACCTGACCG  >  NC_000913_3_pae_pgi/2262933‑2263229                                                                                                                                                      |                                                                                                                                                      ttGGTGACGAAAGTGGCTTCAACTGCCCCCGCCTCTTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAg                                                                                                                                                       <  2:391231/149‑1 (MQ=255)   ggTGGCGAAACGCGCGTCAACTGCCCGCGCCTCTTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCTGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTa                                                                                                                                                     <  2:849239/149‑1 (MQ=255)      gccGAACGTGGCCTCGACGCCCCCCGCGTCGCTCAGACGCGCAGTTGTCATCCCCTGAAGTGTC‑AGCACATCGCTGGCGACGATATTCAGGGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATg                                                                                                                                                 <  2:70303/147‑1 (MQ=255)              tGGCGTCAACTGCCCCCGCCTCTTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTACTCACTGTGCTTTTCGCCCATCATTA‑ATGCCCGGAGt                                                                                                                                         >  2:508994/1‑149 (MQ=255)                gCGTCAACTGCCCCCGCCTCTTTCAGACCCACAGCGTTC‑GCGATTTCTTTTACGAGCACATCGCTGGTGATGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGttc                                                                                                                                       <  1:731897/149‑1 (MQ=255)                 cGTCAACTGCCCCCGCCTCTTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGttct                                                                                                                                      <  1:90350/149‑1 (MQ=255)                  gTCAACTGCCCCCGCCTCTTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGttctt                                                                                                                                     <  2:604838/149‑1 (MQ=255)                   cccagtGCTCCCGCCTTTTTCAGACGCGCAGCGTTCAGTTTTTGATGTGTT‑AGCATATCGATGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGttcttc                                                                                                                                    <  1:31439/144‑1 (MQ=255)                     aaCTGCCCCCGCCTCTTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGATGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTctg                                                                                                                                  <  1:559845/149‑1 (MQ=255)                        tGCCCCCGCCTCTTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑ACCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACCCTGCTTTTCGCCCATCAGTA‑ACGCGCGCAGTTCTTctgctc                                                                                                                               >  2:563287/1‑148 (MQ=255)                                 ctctTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCCGATCGCTGGCGCCGATATCCAGTGTCAGCATTTCGTTGGCGAGCTTCAGCTGCTCACTCGGCTTTTCGCCCATCAGTA‑GTGCGCGAAGTTCTACTACTGGGGTTGCTg                                                                                                                      >  1:712440/1‑149 (MQ=255)                                  tctTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGGTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGa                                                                                                                     <  2:509634/149‑1 (MQ=255)                                  tctTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGa                                                                                                                     >  1:886383/1‑149 (MQ=255)                                  tctTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGCCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGGTGCTGa                                                                                                                     >  1:875438/1‑149 (MQ=255)                                   ctgtCAGACGCGCAGCCTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCCCACTCTGCTTCTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGAc                                                                                                                    <  2:420037/146‑1 (MQ=255)                                    tttCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGGTCCCTGGCGACGATAAAGTTTTCCATCATTTCGTTGTCGAGCTTCAGCTTCTCACGCTGCGTTTCGCCCATCACGA‑CTGCGCGAAGTTCTTCTGGTGTTGGTGCGGACt                                                                                                                   >  1:396376/1‑149 (MQ=255)                                           cgcgCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAgttg                                                                                                            <  1:40890/149‑1 (MQ=255)                                             cgcAGGGTTCGCCTCCTGAAGAGTC‑AGCATATGGCTGGCGACGAGATCCAGTGGCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTATGATTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAgttgtt                                                                                                          <  2:165284/149‑1 (MQ=255)                                               cAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCa                                                                                                        <  1:650402/149‑1 (MQ=255)                                               cAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTGTCGCCCATCAGTA‑ATGCGCGATGTTCTTCTGCTGTTGTTGCTGCCTCCAGCTGTTCa                                                                                                        >  1:99889/1‑149 (MQ=255)                                                                agagTC‑AGCAGATCGCTGGTGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGTTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCt                                                                                       <  1:372543/149‑1 (MQ=255)                                                                agagCC‑AGCAGCTTGCTGGGCGCGTGATCGATTGTCCGCCTGTCGTTCTCGAGTTTGAACTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGcc                                                                                       <  2:68383/149‑2 (MQ=255)                                                                  gtggcggcagTTCGCTGGCGACGATATCCAGTTTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATCCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTc                                                                                      <  2:118846/143‑1 (MQ=255)                                                                    tC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑AGGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGt                                                                                   >  1:896543/1‑149 (MQ=255)                                                                           gATCGCTGGCGAGCATAGCCCGTGTCCGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTgg                                                                             <  2:598984/149‑1 (MQ=255)                                                                                  tgctactatatCCAATTCCAGCATTTTGTTGTCGAGCTTCAGCTTATCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGCCTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCt                                                                      <  2:301788/142‑1 (MQ=255)                                                                                      acgaTGTCCAGTTGCAGCATTTCGTGGTCGGTCTTCAGCTGCTCTCTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCg                                                                  <  2:138383/149‑1 (MQ=255)                                                                                           atCCAGGTTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCa                                                             <  1:602613/149‑1 (MQ=255)                                                                                             ccAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGttctt                                                                                                                                     <  1:797987/75‑1 (MQ=255)                                                                                             ccAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGttctt                                                                                                                                     >  2:797987/1‑75 (MQ=255)                                                                                              cAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCGCAGTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGc                                                          <  2:937974/149‑1 (MQ=255)                                                                                                   tCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGCCCAgg                                                     >  2:203758/1‑148 (MQ=255)                                                                                                   tCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGCCCAgc                                                     >  1:667743/1‑148 (MQ=255)                                                                                                   ccAGCATTTCGCTGTCGAGCTTCATCTTCTCACTGTGCTTTTTGCGCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTTCTGACTGCACTTGGTCAGCAACGGAATCATCGCTCACTACGTGGGTCAGCTGGAGTAGCAGGCCCAGa                                                     <  2:71282/148‑1 (MQ=255)                                                                                                      gCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGCCCAGATGt                                                  >  1:308356/1‑149 (MQ=255)                                                                                                                        tCAGCTGCTCACTCTGCTTTTCGCCCATCAGGA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGTCTGCAGTTGTTCAGCAACGGAATCCTCGCTCAGTACGTGGGTCAGCTGGCGTTGCAGGCCCATATGTTCCTCCGAGCTGgcagca                                >  1:266004/1‑149 (MQ=255)                                                                                                                           gctgctCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGCCCAGATGTTCATCCGAGCTGGCAGCAATa                             >  2:600759/1‑149 (MQ=255)                                                                                                                           gctgctCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGCCCAGATGTTCATCCGAGCTGGCAGCAATa                             >  1:472101/1‑149 (MQ=255)                                                                                                                               ctCCCTCTGCTTTTCGCCCATCCGTA‑CTGCGCGAAATTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCACCGGAATCATCGCTGAATACGTGGGCCAGCGTGCGTAGCCGGCCCAGATGTTCATCCGAGCTGCCACCAATACCgc                         >  2:116775/1‑148 (MQ=255)                                                                                                                               ctCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAgtt                                                                                                             >  1:306729/1‑65 (MQ=255)                                                                                                                               ctCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAgtt                                                                                                             <  2:306729/65‑1 (MQ=255)                                                                                                                                 taCTCTGCCTTTCACCCATCACTA‑ACGCGCGAACTTCTCTTGCTGTTGTTGCTGACTTCAGTTTTTCAGCAACGGAATCATCGCGCAGTACGGGGGTTAGCTGGCGTAGCAGGCCCAGATTTTCATCCGAGCGGGCAGCAATACCAAtt                       <  2:643231/148‑1 (MQ=255)                                                                                                                                 cACTCTGCTTTTCGCCCATCAATA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTgg                                                                    <  1:413022/104‑1 (MQ=255)                                                                                                                                 cACTCTGCTTTTCGCCCATCAATA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTgg                                                                    <  1:412997/104‑1 (MQ=255)                                                                                                                                 cACTCTGCTTTTCGCCCATCAATA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTgg                                                                    >  2:413022/1‑104 (MQ=255)                                                                                                                                 cACTCTGCTTTTCGCCCATCAATA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTgg                                                                    >  2:412997/1‑104 (MQ=255)                                                                                                                                   ctctGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGCCCAGATGTTCATCCGAGCTGGCAGCAATACCGATTGc                     <  1:361925/149‑1 (MQ=255)                                                                                                                                          tttAGCCCATAAGTATATG‑GCGATGTTCTGCTGGTGTGTTGGCGCATTTCAGTTGTTCAGCAAGCGAAGCCTCGCTCAGTTCGTGGGGTAGCTGGCGTCGCAGGCCCAGATGTTCATCCGAGCTGGCAGCAACACTGACTGCCACGTAc              <  2:270739/149‑1 (MQ=255)                                                                                                                                             cGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGCCCAGATGTTCATCCGAGCTGGCAGCAATACCGATTGCCACGTACGCt           <  2:886383/149‑1 (MQ=255)                                                                                                                                                  aTCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGCCCAGATGTTCATCCGAGCTGGCAGCAATACCGATTGCCACGTACGCTACCTg      >  1:770677/1‑149 (MQ=255)                                                                                                                                                  aTCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGCCCAGATGTTCATCCGAGCTGGCAGCAATACCGATTGCCACGTACCCTACCTg      >  2:918295/1‑149 (MQ=255)                                                                                                                                                      gTA‑ATGCGCGAAGCTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAAGCCCAGATGTTCATCCGAGCTGGCAGCAATACCGATTGCCACGTACGCTACATGACCg  >  1:270358/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                                      TTGGTGACGAAAGTGGCGTCAACTGCCCCCGCCTCTTTCAGACGCGCAGCGTTCAGCGCCTGAAGAGTC‑AGCAGATCGCTGGCGACGATATCCAGTGTCAGCATTTCGTTGTCGAGCTTCAGCTGCTCACTCTGCTTTTCGCCCATCAGTA‑ATGCGCGAAGTTCTTCTGCTGTTGTTGCTGACTTCAGTTGTTCAGCAACGGAATCATCGCTCAGTACGTGGGTCAGCTGGCGTAGCAGGCCCAGATGTTCATCCGAGCTGGCAGCAATACCGATTGCCACGTACGCTACCTGACCG  >  NC_000913_3_pae_pgi/2262933‑2263229

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑