Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	349,624	C→T	intergenic (+52/‑388)	prpB → / → prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	349,624	0	C	T	100.0%	100.4 / NA	36	intergenic (+52/‑388)	prpB/prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (14/22);  total (14/22)

ACCATGCAGACCCGCAACGAGCTGTACGAAAGCATCAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTT  >  NC_000913_3_pae_tpiA/349477‑349722                                                                                                                                                    |                                                                                                   acCATGCAGACCCGCAACGAGCTGTACGAAAGCATCAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGa                                                                                                  <  4:195077/150‑1 (MQ=255) acCATGCAGACCCGCAACGAGCTGTACGAAAGCATCAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGa                                                                                                  <  1:462504/150‑1 (MQ=255)    aTGCAGACCCGCAACGAGCTGTACGAAAGCATCAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACtt                                                                                               <  3:167239/150‑1 (MQ=255)            ccGCAACGAGCTGTACGAAAGCATCAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGcc                                                                                       >  3:37943/1‑150 (MQ=255)                   acgCTGTACGAAAGCATCAACTACTACCCGTCCGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAACAACGACCGTTGATTGTATTCCACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACgggg                                                                                <  2:318884/148‑1 (MQ=37)                     gCTGTACGAAAGCATCAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTg                                                                              >  2:699638/1‑150 (MQ=255)                     gCTGTACGAAAGCATCAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTg                                                                              <  3:461215/150‑1 (MQ=255)                            gAAAGCATCAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGaa                                                                       <  3:168533/150‑1 (MQ=255)                                  aTCAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGACTGGATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGCCTTATCAGGCCCACGGGGTGCACTGAACTGTAg                                                                 >  1:270373/1‑150 (MQ=37)                                    cAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACggg                                                                                 >  2:898531/1‑130 (MQ=255)                                    cAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACggg                                                                                 <  1:898531/132‑3 (MQ=255)                                     aaCTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGt                                                                               >  1:360602/1‑133 (MQ=255)                                     aaCTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGt                                                                               <  2:360602/133‑1 (MQ=255)                                       ctactaCCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCgg                                                            <  2:104123/150‑1 (MQ=255)                                           tacCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATaa                                                        <  1:788230/150‑1 (MQ=255)                                           tacCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATaa                                                        >  2:749686/1‑150 (MQ=255)                                              cAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGAc                                                     >  1:632981/1‑150 (MQ=255)                                                    gAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACgcatag                                               <  1:277427/150‑6 (MQ=21)                                                        agaAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTc                                           <  2:307206/150‑1 (MQ=21)                                                          aaGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACCGCCGATGCCTGATGCGCCGCCGACGTGACCTATCACGCGTACGGGGTGCATTGAACTGTAGGTCGGATAAGACGCATAGCGTCGc                                         <  1:322698/150‑1 (MQ=21)                                                          aaGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGc                                         >  3:40539/1‑150 (MQ=18)                                                          aaGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGc                                         <  2:632981/150‑1 (MQ=18)                                                              tCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGt                                                                   >  1:372263/1‑120 (MQ=25)                                                              tCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGt                                                                   <  2:372263/120‑1 (MQ=25)                                                                     ccTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACgg                                                                                  <  3:11764/98‑2 (MQ=255)                                                                     ccTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACgg                                                                                  >  4:11764/1‑97 (MQ=255)                                                                      cTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCa                                                                            <  2:481471/103‑1 (MQ=25)                                                                      cTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCa                                                                            >  1:481471/1‑103 (MQ=25)                                                                        gTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACggg                                                                                 >  2:71775/1‑94 (MQ=25)                                                                        gTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACggg                                                                                 <  1:71775/96‑3 (MQ=25)                                                                                         tgaaatgaaaAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTgc          <  2:270373/150‑2 (MQ=11)                                                                                              tAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGa     <  1:699638/150‑1 (MQ=11)                                                                                               aaaaaaCGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGAc    <  2:832457/150‑1 (MQ=11)                                                                                                 aaaaCGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACtt  >  1:226328/1‑150 (MQ=11)                                                                                                             gATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAg                                                                 <  1:181802/75‑1 (MQ=11)                                                                                                             gATTGTATTCGACAGCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAg                                                                 >  2:181802/1‑75 (MQ=11)                                                                                                                                                    |                                                                                                   ACCATGCAGACCCGCAACGAGCTGTACGAAAGCATCAACTACTACCAGTACGAAGAGAAGCTCGACAACCTGTTTGCCCGTAGCCAGGTGAAATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTT  >  NC_000913_3_pae_tpiA/349477‑349722

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑