Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006881	2,197,769	G→A	H123H (CAC→CAT)	U712_11010 ←	Chorismate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	2,197,769	0	G	A	100.0%	189.1 / NA	61	H123H (CAC→CAT)	U712_11010	Chorismate synthase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (25/36);  total (25/36)

TGCGCCAATTTGCAATACGTGACCTGCCACCTTAATGCCGAGCTCAGAAAGAATCTTTTTAGCGACAGCTCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAGCGCTCAAGCACATTTCTCATATCACGGTGATTATATTTAATCGCTCCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATTTGGCGCTTCATTTCCTTTTCTTCATCCTCTGTAATCGGAGCCGCACCCATGATTTTTGTCCAATGCT  >  CP006881/2197634‑2197893                                                                                                                                        |                                                                                                                             agcgcCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGa                                                                                                                           <  6:172034/138‑1 (MQ=255) agcgcCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGa                                                                                                                           <  2:423868/138‑1 (MQ=255)    gcCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATta                                                                                                                        >  1:236038/1‑139 (MQ=255)    gcCAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATta                                                                                                                        >  6:271173/1‑139 (MQ=255)      cAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATtata                                                                                                                      <  8:429960/139‑1 (MQ=255)      cAATTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATtata                                                                                                                      <  2:236038/139‑1 (MQ=255)        aTTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATAtt                                                                                                                    <  6:279050/139‑1 (MQ=255)        aTTTGCAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATAtt                                                                                                                    <  4:56044/139‑1 (MQ=255)             cAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAAt                                                                                                                <  4:81987/138‑1 (MQ=255)             cAACACGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTATTTAGCTACAGCCCCTGCCGCCACTCTGTCAGTTGGTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAAtt                                                                                                               >  3:360783/1‑138 (MQ=255)              aacaCGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAAttg                                                                                                              <  5:218238/136‑3 (MQ=255)                caCGTGGCCCGCCACCTTAATGCCAAGCTCAGAATGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGca                                                                                                            <  5:354610/138‑2 (MQ=255)                caCGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTTCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGca                                                                                                            <  5:212272/138‑2 (MQ=255)                caCGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGca                                                                                                            <  6:439260/138‑2 (MQ=255)                caCGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGca                                                                                                            <  1:80139/138‑2 (MQ=255)                caCGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGca                                                                                                            <  5:271173/138‑2 (MQ=255)                caCGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGca                                                                                                            <  7:368578/138‑2 (MQ=255)                caCGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGca                                                                                                            <  1:357595/138‑2 (MQ=255)                caCGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATATTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGca                                                                                                            <  7:169235/138‑2 (MQ=255)                 aCGTGGCCCGCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGcac                                                                                                           <  1:319475/139‑3 (MQ=255)                        ccgCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTaa                                                                                                    <  2:200984/137‑1 (MQ=255)                         cgCCACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAg                                                                                                   <  5:290697/138‑1 (MQ=255)                            cACCTTAATGCCAAGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGt                                                                                                  >  7:204382/1‑137 (MQ=255)                              ccTTAATGCCACGCTCCCCAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTGTCCCTTGCTGAAGAACGCGCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGc                                                                                              <  1:364140/139‑1 (MQ=255)                                         aGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCCCTCGGACAGTTGTTTCCCTTGCTGAAGCACGCTCAAGCACAATTCTCATATCACGAAGATTATATTTAATAGCACCGATTAAGTCAGCGTGcccgagtc                                                                                   >  4:276453/1‑134 (MQ=255)                                         aGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACGTTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGtc                                                                                   >  6:263872/1‑139 (MQ=255)                                         aGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCCCGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGtc                                                                                   >  1:182076/1‑139 (MQ=255)                                         aGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGca                                                                                                            >  1:310693/1‑113 (MQ=255)                                         aGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGca                                                                                                            <  2:310693/114‑2 (MQ=255)                                         aGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGtc                                                                                   >  5:75606/1‑139 (MQ=255)                                         aGCTCAGAAAGAATCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGtc                                                                                   >  5:223694/1‑139 (MQ=255)                                          ccTCAGCAAGACTCTTTTTAGCGACAGCCCCTGCCGCCACTCTGACAGGTGTTTCCCTTGCAGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGGTTAAGTCAGCGTGCCCAGGtct                                                                                  <  2:184932/138‑1 (MQ=255)                                                   gaaTCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGa                                                                         <  3:397749/139‑1 (MQ=255)                                                   gaaTCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGa                                                                         <  7:156886/139‑1 (MQ=255)                                                     aTCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGAtt                                                                                                                         <  3:287560/89‑1 (MQ=255)                                                     aTCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGAtt                                                                                                                         >  4:287560/1‑89 (MQ=255)                                                     aTCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCa                                                                                                >  5:286975/1‑114 (MQ=255)                                                     aTCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCa                                                                                                <  6:286975/114‑1 (MQ=255)                                                     aTCTTTTTAGCTACAGCCCCTGCCGCCACTCTGACAGTTGTTTCCCTATCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGaaa                                                                       >  7:52533/1‑139 (MQ=255)                                                        tttttAGCTCCAGCCAATTCCGCCACTCTGACAGTTGTTTCCGTTGCTTAAGAAAGCTCCAGCACATAAGTAATATCACGATGATTATATTTAATTGCACCGGTTAAGTCAGCGAGCCGAGGTCACGGTCTGGAAAtct                                                                    >  2:295233/1‑137 (MQ=255)                                                                          gccgccACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCttt                                                   >  6:398283/1‑138 (MQ=255)                                                                          gccgccACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGAATATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATATCCtttt                                                  >  7:338344/1‑139 (MQ=255)                                                                           ccgccACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTttc                                                 <  1:214554/139‑1 (MQ=255)                                                                               cACTCTGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGGGCGTCAGTTCCttttggtca                                             >  8:269881/1‑134 (MQ=255)                                                                                  tctGACAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTGCAGTTCCGTTTGTTAATca                                          >  2:406291/1‑138 (MQ=255)                                                                                      aCAGTTGTTTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATCTTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCttc                                        <  1:406291/137‑1 (MQ=255)                                                                                      aCAGTTGATTCCCTTGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGGGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCAtcttct                                       <  5:90409/138‑1 (MQ=255)                                                                                                    tGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGcg                        >  3:183477/1‑138 (MQ=255)                                                                                                    tGCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCGTCATCTTCTGTAATCGGAGCGGcg                        >  7:60014/1‑138 (MQ=255)                                                                                                     gCTGAAGAACGCTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGcg                        <  4:222091/138‑2 (MQ=255)                                                                                                              cgcTCAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTACTTTTGTTCATATTCTGTTATCGTAGCTGCGCCCATGAttt              >  7:322929/1‑139 (MQ=255)                                                                                                                  cAAGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGt          <  1:321058/139‑1 (MQ=255)                                                                                                                   aaGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCAt                                            >  7:172680/1‑104 (MQ=255)                                                                                                                   aaGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCAt                                            <  8:172680/104‑1 (MQ=255)                                                                                                                   aaGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTg           <  8:180844/137‑1 (MQ=255)                                                                                                                   aaGCACATTTCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTc         <  7:56492/139‑1 (MQ=255)                                                                                                                      cacaTTTCTCCTATAAAGATGATTATATTTATTTGCAACGTTTAAGTCATAGTGCCCATGTCTCGGTCTTGAAAGCTGGAGCTTCATTTCCTTTTCTTCATATGCTGTAATCGGATCGGCGCCCATGATTTTTGTCCaa      <  7:278346/139‑1 (MQ=255)                                                                                                                           ttCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGtct                                                                                  >  1:218247/1‑58 (MQ=255)                                                                                                                           ttCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGtct                                                                                  <  2:218247/58‑1 (MQ=255)                                                                                                                           ttCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCAATTACTTTTCTTAATATTATGTAATAGGAGCGGCGCCCCATATTTTTGTCCTATgat  >  4:77790/1‑136 (MQ=255)                                                                                                                           ttCTCATATCACGATGATTATATTTAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCGACTCTTCCTTTTCGTGATCATCTGTAATCGGAGCGGCGCCCCATATTTTTTTCCAAGGCt  >  5:425864/1‑138 (MQ=255)                                                                                                                                        |                                                                                                                             TGCGCCAATTTGCAATACGTGACCTGCCACCTTAATGCCGAGCTCAGAAAGAATCTTTTTAGCGACAGCTCCTGCCGCCACTCTGACAGTTGTTTCCCTTGCTGAAGAGCGCTCAAGCACATTTCTCATATCACGGTGATTATATTTAATCGCTCCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATTTGGCGCTTCATTTCCTTTTCTTCATCCTCTGTAATCGGAGCCGCACCCATGATTTTTGTCCAATGCT  >  CP006881/2197634‑2197893

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑