Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006881	2,197,106	T→A	A344A (GCA→GCT)	U712_11010 ←	Chorismate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	2,197,106	0	T	A	100.0%	196.2 / NA	63	A344A (GCA→GCT)	U712_11010	Chorismate synthase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (24/39);  total (24/39)

CCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATTCCTGTCG  >  CP006881/2196974‑2197236                                                                                                                                     |                                                                                                                                   ccTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAg                                                                                                                              <  2:247110/139‑1 (MQ=255) ccTCGACAGTTTTCTCATATTCTCAACATTTTCTCTAATGCGGTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAg                                                                                                                              <  8:337331/139‑1 (MQ=255) ccTCGACAGCTTTCTCATAATCGCCACATATACGCTAATGCCGTCAATATGACCTAAGCCGACTTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAg                                                                                                                              <  3:164238/139‑1 (MQ=255)   tCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCt                                                                                                                            >  5:261707/1‑139 (MQ=255)         gTTTTCTCATATTCTCCATTTTTTCTCTTATGCGGTCAACTTCAACTAATCCCAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGa                                                                                                                      <  1:340057/139‑1 (MQ=255)         gTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGa                                                                                                                      <  5:169225/139‑1 (MQ=255)         gTTTCCTCATATTCTCCACATTTTCTCTAATGCGGTCAATTTGATCAAATCCGACTTGTTCAACGACTGCGGTCTCAATCTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGa                                                                                                                      <  7:58997/139‑1 (MQ=255)                    ttCTCCACATTTTCTCTAATGCGGTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGCCTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGc                                                                                                           >  6:405785/1‑139 (MQ=255)                         cacaTTTTCTCTAATGCGGTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTgg                                                                                                        <  8:424264/137‑1 (MQ=255)                                      aTGCGGTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCt                                                                                          <  1:35253/138‑1 (MQ=255)                                           gTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGa                                                                                                                      <  1:415186/105‑1 (MQ=255)                                           gTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGa                                                                                                                      <  1:365963/105‑1 (MQ=255)                                           gTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGa                                                                                                                      <  1:359962/105‑1 (MQ=255)                                           gTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGa                                                                                                                      >  2:415186/1‑105 (MQ=255)                                           gTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGa                                                                                                                      >  2:359962/1‑105 (MQ=255)                                           gTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGa                                                                                                                      >  2:365963/1‑105 (MQ=255)                                           gTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGtt                                                                                    >  7:301636/1‑139 (MQ=255)                                           gTCAATTTGATCTAATCCGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGATCAATGCTGGCAGAAAACGGTTCTTTCGtt                                                                                    >  6:448148/1‑139 (MQ=255)                                              aaTTTGATCTAATCCGACTTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTc                                                                                  <  8:404363/137‑1 (MQ=255)                                                 tttaTCTATTCCCAATTGTTCAACCCCTGGGTGCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAat                                                                               <  8:395324/135‑1 (MQ=255)                                                         atccGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAACCGGTTCTTTCGTTTCAATATCGAca                                                                        <  3:375975/135‑2 (MQ=255)                                                          tccGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGTACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACtt                                                                     >  1:49339/2‑139 (MQ=255)                                                          tccGAATTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACtt                                                                     >  3:163237/2‑139 (MQ=255)                                                              aaTTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCa                                                                 <  4:315015/139‑1 (MQ=255)                                                              aaTTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCa                                                                 <  3:155135/139‑1 (MQ=255)                                                              aaTTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCa                                                                 <  3:150614/139‑1 (MQ=255)                                                               aTTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCa                                                                 <  2:88981/138‑1 (MQ=255)                                                               aTTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAg                                                                <  6:150290/139‑1 (MQ=255)                                                               aTTGTTCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAg                                                                <  6:132045/139‑1 (MQ=255)                                                                ttGTTCAACGACTGCGTTCGCAAATTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGc                                                               <  1:233827/139‑1 (MQ=255)                                                                   ttCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGaa                                                                                                   <  2:383562/100‑1 (MQ=255)                                                                   ttCAACGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGaa                                                                                                   >  1:383562/1‑100 (MQ=255)                                                                        cGACTGCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTtata                                                       >  5:214659/1‑139 (MQ=255)                                                                          aCTGCGTTCGCAATTTCCCACGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACa                                                     <  1:160536/139‑1 (MQ=255)                                                                             gCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGa                                                                                                                      >  5:13872/1‑71 (MQ=255)                                                                             gCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGa                                                                                                                      <  6:13872/71‑1 (MQ=255)                                                                             gCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCtt                                                                                         >  6:78920/1‑100 (MQ=255)                                                                             gCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCtt                                                                                         <  5:78920/100‑1 (MQ=255)                                                                             gCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCa                                                                 <  1:237043/124‑1 (MQ=255)                                                                             gCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCa                                                                 >  2:237043/1‑124 (MQ=255)                                                                             gCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCa                                                                 >  8:177891/1‑124 (MQ=255)                                                                             gCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCa                                                                 <  7:177891/124‑1 (MQ=255)                                                                             gCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAg                                                  >  7:321943/1‑139 (MQ=255)                                                                             gCGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGGTTATACAAAg                                                  >  5:288502/1‑139 (MQ=255)                                                                              cGTTCGCAATTTCCCAAGCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGt                                                 <  3:130671/139‑1 (MQ=255)                                                                                            caagCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGATCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCa                                   <  6:184646/136‑1 (MQ=255)                                                                                               gCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATcga                                                                          <  4:408099/97‑3 (MQ=255)                                                                                               gCGACAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATcga                                                                          >  3:408099/1‑95 (MQ=255)                                                                                                   cAGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTcc                            >  4:320722/1‑139 (MQ=255)                                                                                                    aGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCcg                           <  3:258062/139‑1 (MQ=255)                                                                                                    aGCCGCTTCAGCGACTACACTTGCCGCAGGAACAGAACAGCTGTCTGAACGTTCAATGCTGGCACAAAACGGTTCTTTCGTTTCAATATCGACACTATTCAGCGGATTATACAAAGTCGTAATCGGCTTCATGACACcg                           >  2:229060/1‑139 (MQ=255)                                                                                                      ccGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCcgcg                         <  8:301636/139‑1 (MQ=255)                                                                                                      ccGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCcgcg                         <  3:180980/139‑1 (MQ=255)                                                                                                      ccGCTTCAGCGACTACACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCcgcg                         <  4:110896/139‑1 (MQ=255)                                                                                                                   tacACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGc                                                               >  7:342644/1‑88 (MQ=255)                                                                                                                   tacACTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGc                                                               <  8:342644/88‑1 (MQ=255)                                                                                                                     cacTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGc            <  1:229060/137‑1 (MQ=255)                                                                                                                     cacTTGCCGCAGGAACAGCACAGCTGTCTGAACGTTAAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCAt          <  6:292195/139‑1 (MQ=255)                                                                                                                     cacTTGCCGCAGGAACAGCACAGCGGTCTGAACGGTCAATGATGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCa           <  2:1517/138‑1 (MQ=255)                                                                                                                        ttGCCGCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATccc       >  6:59107/1‑139 (MQ=255)                                                                                                                             gCAGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATCCCTgtcg  >  4:256493/1‑139 (MQ=255)                                                                                                                               aGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCa                                                                 <  6:303895/74‑1 (MQ=255)                                                                                                                               aGGAACAGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCGACACTTTTCa                                                                 >  5:303895/1‑74 (MQ=255)                                                                                                                                     |                                                                                                                                   CCTCGACAGTTTTCTCATATTCTCCACATTTTCTCTAATGCGGTCGATTTGATCTAAGCCGAATTGTTCAACGACTGCGTTCGCAATCTCCCATGCGACAGCCGCTTCAGCTACTACACTTGCCGCAGGCACTGCACAGCTGTCTGAACGTTCAATGCTGGCAGAAAACGGTTCTTTCGTTTCAATATCTACGCTTTTCAGCGGTTTATACAAAGTCGGAATCGGCTTCATGACTCCGCGGACAACAATCGGCATTCCTGTCG  >  CP006881/2196974‑2197236

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑