Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,956,875	G→A	*515* (TAG→TAA)	ilvA →	l‑threonine dehydratase, biosynthetic, also known as threonine deaminase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,956,875	0	G	A	100.0%	217.6 / NA	67	*515* (TAG→TAA)	ilvA	l‑threonine dehydratase, biosynthetic, also known as threonine deaminase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/40);  total (27/40)

GACTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAGGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGCACA  >  NC_000913/3956741‑3956998                                                                                                                                       |                                                                                                                            gACTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCGCGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaa                                                                                                                         >  2:1139976/1‑139 (MQ=255) gACTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaa                                                                                                                         >  1:1798796/1‑139 (MQ=255) gACTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaa                                                                                                                         >  1:164044/1‑139 (MQ=255)   cTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaaaa                                                                                                                       <  2:1524841/139‑1 (MQ=255)   cTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGaaaa                                                                                                                       <  2:1020794/139‑1 (MQ=255)            cgTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGAt                                                                                                              <  2:1576243/139‑1 (MQ=255)            cgTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGAt                                                                                                              >  2:1328256/1‑139 (MQ=255)             gTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATa                                                                                                             >  1:1787959/1‑139 (MQ=255)             gTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATa                                                                                                             <  1:1736958/139‑1 (MQ=255)              tACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAg                                                                                                            <  2:1787959/139‑1 (MQ=255)                cTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAgcg                                                                                                          <  2:164044/139‑1 (MQ=255)                     ggcgTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCACTAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgcttcg                                                                                                     <  1:83500/139‑1 (MQ=255)                     ggcgTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgcttcg                                                                                                     >  1:654190/1‑139 (MQ=255)                       cgTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgcttcgct                                                                                                   >  2:1137006/1‑139 (MQ=255)                         ttCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTa                                                                                                 <  2:755415/139‑1 (MQ=255)                          tCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTAt                                                                                                <  2:349096/139‑1 (MQ=255)                           cGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATc                                                                                               <  1:520335/139‑1 (MQ=255)                              aCTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAgg                                                                                            <  1:1786758/139‑1 (MQ=255)                                     gACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTAccc                                                                                     <  1:1724677/139‑1 (MQ=255)                                        cATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCcgcg                                                                                  <  2:1482594/139‑1 (MQ=255)                                          tGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCcgcgcg                                                                                <  1:1519079/139‑1 (MQ=255)                                            aaCCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGAc                                                                              <  1:1137006/139‑1 (MQ=255)                                               cGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAAc                                                                           <  1:429723/139‑1 (MQ=255)                                                ggATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACg                                                                          <  1:1700256/139‑1 (MQ=255)                                                         aaCCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAgcg                                                                                                          <  2:1392568/98‑1 (MQ=255)                                                         aaCCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAgcg                                                                                                          >  1:1392568/1‑98 (MQ=255)                                                               gCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCgg                                                           >  2:655962/1‑139 (MQ=255)                                                               gCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCgg                                                           >  1:593206/1‑139 (MQ=255)                                                               gCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCgg                                                           <  2:1798796/139‑1 (MQ=255)                                                                   aaTGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCaaa                                                       <  2:593206/139‑1 (MQ=255)                                                                    aTGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCaaaa                                                      <  1:801305/139‑1 (MQ=255)                                                                    aTGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCaaaa                                                      <  2:654190/139‑1 (MQ=255)                                                                             gCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGa                                             <  1:655962/139‑1 (MQ=255)                                                                              cTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGaa                                            >  1:1408477/1‑139 (MQ=255)                                                                                 cGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGt                                                               >  2:293326/1‑117 (MQ=255)                                                                                 cGATTGCCACGACGAAACAAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGt                                                               <  1:293326/117‑1 (MQ=255)                                                                                      gCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATg                                                                                                                    <  1:1263844/59‑1 (MQ=255)                                                                                      gCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATg                                                                                                                    >  2:1263844/1‑59 (MQ=255)                                                                                      gCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCaa                                    >  2:727634/1‑139 (MQ=255)                                                                                       ccACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGAc                                                                              >  1:1334306/1‑96 (MQ=255)                                                                                       ccACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGAc                                                                              <  2:1334306/96‑1 (MQ=255)                                                                                          cgacgaAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAg                                <  2:1408477/139‑1 (MQ=255)                                                                                           gacgaAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGc                               <  1:730151/139‑1 (MQ=255)                                                                                            acgaAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCg                              >  2:1217463/1‑139 (MQ=255)                                                                                            acgaAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCg                              >  2:360341/1‑139 (MQ=255)                                                                                                 aCCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGCAAAATGCCTGATAGCGCTTCGCTCATCAGGCCTACCCCCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCTAGAATGCCTCAATTAGCGGCTCa                         >  1:1082853/1‑139 (MQ=255)                                                                                                      tAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAg                    >  1:1296942/1‑139 (MQ=255)                                                                                                       aaCCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgctt                                                                                                       >  2:1468318/1‑55 (MQ=255)                                                                                                       aaCCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgctt                                                                                                       <  1:1468318/55‑1 (MQ=255)                                                                                                       aaCCCGGCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGc                   <  1:360341/139‑1 (MQ=255)                                                                                                             gCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgcttcg                                                                                                     >  2:71266/1‑51 (MQ=255)                                                                                                             gCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgcttcg                                                                                                     <  1:71266/51‑1 (MQ=255)                                                                                                             gCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgct                                                                                                        >  1:502579/1‑48 (MQ=255)                                                                                                             gCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGcgct                                                                                                        <  2:502579/48‑1 (MQ=255)                                                                                                             gCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTAt                                                                                                >  1:1460283/1‑56 (MQ=255)                                                                                                             gCGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTAt                                                                                                <  2:1460283/56‑1 (MQ=255)                                                                                                              cGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGAc                                                                              >  1:1209428/1‑73 (MQ=255)                                                                                                              cGTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGAc                                                                              <  2:1209428/73‑1 (MQ=255)                                                                                                               gTTCAGGTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCttttt           <  1:845800/139‑1 (MQ=255)                                                                                                                    ggTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGt                                                                         <  1:10861/72‑1 (MQ=255)                                                                                                                    ggTTCTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGt                                                                         >  2:10861/1‑72 (MQ=255)                                                                                                                        cTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGcaca  <  2:68911/139‑1 (MQ=255)                                                                                                                        cTTTTTGGCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGcaca  <  1:727634/139‑1 (MQ=255)                                                                                                                               gCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGc                            >  2:1769518/1‑106 (MQ=255)                                                                                                                               gCGGGTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGc                            <  1:1769518/106‑1 (MQ=255)                                                                                                                                   gTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAAc                                                                           >  1:629289/1‑55 (MQ=255)                                                                                                                                   gTTAAGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAAc                                                                           <  2:629289/55‑1 (MQ=255)                                                                                                                                       |                                                                                                                            GACTACGGGCGCGTACTGGCGGCGTTCGAACTTGGCGACCATGAACCGGATTTCGAAACCCGGCTGAATGAGCTGGGCTACGATTGCCACGACGAAACCAATAACCCGGCGTTCAGGTTCTTTTTGGCGGGTTAGGGAAAAATGCCTGATAGCGCTTCGCTTATCAGGCCTACCCGCGCGACAACGTCATTTGTGGTTCGGCAAAATCTTCCAGAATGCCTCAATTAGCGGCTCATGTAGCCGCTTTTTCTGCGCACA  >  NC_000913/3956741‑3956998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑