Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,528,377	A→C	100%	F284C (TTT→TGT)	envZ ←	sensory histidine kinase in two‑component regulatory system with OmpR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,528,377	0	A	C	100.0%	156.0 / ‑6.7	46	F284C (TTT→TGT)	envZ	sensory histidine kinase in two‑component regulatory system with OmpR
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base C (24/21);  total (25/21)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACCAGGCGCGATTCGGCTCCGTTCCGCTGCTGACTTTGATCCAGCCATTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTACCCCCGCCATCAGCAGCGTGCGGTCATCCGCCAGTTGCTTAACACCAGCCGCCATATGGTTAAAGGCACGGGTAACGGAACGCACCTCCGAAGCGCCATACTCACGCAGCGGCGGCGGAATAATCCCTTTACCA  >  CP009273/3528123‑3528640                                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                                        aCCAGGCGCGATTCGGCTCCGTTCCGCTGCTGACTTTGATCCAGCCATTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCACGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTATCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTACCCGGTGCGCAGCTCGTCGACACACTGCTCAAAGATGGCGt                                                                                                                                                                                                                                                       >  1:69274/1‑273 (MQ=255)                                            gCCATTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCa                                                                                                                                                                                                                   >  1:118432/1‑266 (MQ=255)                                                ttGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATa                                                                                                                                                                                                               <  2:118432/266‑1 (MQ=255)                                                                                                               aTTGTCACTTCAATGATGCCGGGGTAAAGAGCGGTTTCAATTTCCCGCTCATAGCAACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTgctcg                                                                                                                                                                                                  <  1:161625/216‑1 (MQ=255)                                                                                                                                              cgGTTTCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCt                                                                                                                                                                                                                       >  2:504946/1‑164 (MQ=255)                                                                                                                                               ggTTTCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGtt                                                                                                                                                                                                                                                      >  1:227038/1‑132 (MQ=255)                                                                                                                                                gTTTCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTcatcat                                                                                                                                                                                          >  1:442293/1‑191 (MQ=255)                                                                                                                                                  ttCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCa                                                                                                                                                                                                                   <  1:504953/164‑1 (MQ=255)                                                                                                                                                   tCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCAc                                                                                                                                                                                                                                                  <  2:227036/132‑1 (MQ=255)                                                                                                                                                    cAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCa                                                                                                                                                                                      <  2:442286/191‑1 (MQ=255)                                                                                                                                                                 aTAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGt                                                                                                                                                                                                                                                       >  1:495229/1‑113 (MQ=255)                                                                                                                                                                     ccACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCa                                                                                                                                                                                                                                                   <  2:495222/113‑1 (MQ=255)                                                                                                                                                                         tttCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTACCCCCGCCATCAGCAGCGTGCGGTCATCCGCCAGTTGCTTAACACAAGCAGCCAAATgg                                                                             >  1:357360/1‑275 (MQ=255)                                                                                                                                                                                            accGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATAGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGt                                                                                                                                                         >  1:397088/1‑180 (MQ=255)                                                                                                                                                                                                aGTACTTCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTgcgc                                                                                                                                                     <  2:397082/180‑1 (MQ=255)                                                                                                                                                                                                  tACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGt                                                                                                                                                                                                                                                       >  1:537250/1‑80 (MQ=255)                                                                                                                                                                                                   aCTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTGATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTACCCCCGCCATCAGCAGCGTGCGGTCATCCGCCAGTTGCTTAACACCAGCCGCCATATGGTTAAAGGCACGGGTAACGGAACGCAc                                                   <  1:298435/275‑1 (MQ=255)                                                                                                                                                                                                      gCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCa                                                                                                                                                                                                                                                   <  2:537242/80‑1 (MQ=255)                                                                                                                                                                                                       cATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCt                                                                                                                                                                                                                       >  1:54478/1‑107 (MQ=255)                                                                                                                                                                                                       cATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTCACTTACCCCCGCCATCAGCAGCGTGCGGTCATCCGCCAGTTGCTTAACACCAgccc                                                                                     >  1:2759/1‑236 (MQ=255)                                                                                                                                                                                                           aaGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCa                                                                                                                                                                                                                   <  2:54478/107‑1 (MQ=255)                                                                                                                                                                                                                 cGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGCTACACTGCTCAATGATGGCGTTGCACTCTTCGCTATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCCGGCGAATACGCGTCAGCGGCGTGCGCaa                                                                                                                                                   >  1:199946/1‑165 (MQ=255)                                                                                                                                                                                                                 cGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGa                                                                                                                                                                                                                               >  1:245158/1‑89 (MQ=255)                                                                                                                                                                                                                 cGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTg                                                                                                                                                                                                      >  2:345880/1‑114 (MQ=255)                                                                                                                                                                                                                 cGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGaa                                                                                                                                                                         >  2:450073/1‑143 (MQ=255)                                                                                                                                                                                                                   ccATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCAc                                                                                                                                                                                                                                                  >  1:125304/1‑68 (MQ=255)                                                                                                                                                                                                                     atgtCCATCGGCATCGCGTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCg                                                                                                                                               <  2:199944/162‑1 (MQ=255)                                                                                                                                                                                                                     aTTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTg                                                                                                                                                                                                                                                                     <  2:82434/47‑1 (MQ=255)                                                                                                                                                                                                                     aTTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGa                                                                                                                                                                                                                           <  2:245156/89‑1 (MQ=255)                                                                                                                                                                                                                     aTTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTgctcg                                                                                                                                                                                                  <  1:345885/114‑1 (MQ=255)                                                                                                                                                                                                                     aTTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATAcg                                                                                                                                                                     <  1:450080/143‑1 (MQ=255)                                                                                                                                                                                                                       ttCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCtt                                                                                                                                                                                                                                              <  2:125303/68‑1 (MQ=255)                                                                                                                                                                                                                                         cccGGTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTACCCCCGCCATCAGCAGCGAGCGGTCATCCGCCAGTTGCTTAACACCAGCCGCCATATGGTTAAAGGCACGGGTAACGGAACGCACCTCCGAAGCGCCAAACTCACGCAGCGCAGGCGGaata              >  1:353995/1‑274 (MQ=255)                                                                                                                                                                                                                                             gTGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGaa                                                                                                                                                                         >  1:408/1‑115 (MQ=255)                                                                                                                                                                                                                                              tGCGCAGGTAGTCGTTAAACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTAc                                                                                                                                       >  1:191094/1‑148 (MQ=255)                                                                                                                                                                                                                                              tGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTAcccc                                                                                                                                    >  1:366081/1‑151 (MQ=255)                                                                                                                                                                                                                                              tGCGCAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTACCCCCGCCATCAGCAGCGTGCGGTCATCCGCCAGTTNCTTAACACCAGCCGCCATAGGGTTAAAGCACCGGTTACCGGACCGCCCCTCCGAAGCCCCAAACCAACGCAGCGGAGGCGAAAAAATCCCt        >  1:438504/1‑275 (MQ=255)                                                                                                                                                                                                                                                 gcAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATAcg                                                                                                                                                                     <  2:408/115‑1 (MQ=255)                                                                                                                                                                                                                                                  cAGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTACCCCCGcc                                                                                                                                <  2:366076/151‑1 (MQ=255)                                                                                                                                                                                                                                                   aGGTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCCGCGGCGTGCGCAAGTCGTGACTTACCCCCGCCATCAGCAGCGTGCGGTCATCCGCCAGTAGCTTAACACCAGCCGCCATATGGTTAAAGGCACGGGTAACGGAACGCACCTCCGAAGCCCCATACTCACGCAGCAGCCGCGGAATAATcccataac    >  1:297316/1‑269 (MQ=255)                                                                                                                                                                                                                                                    ggTAGTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGCTCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTACCCCCGCCATCAGCAGCGTGCGGTCATCCGCCAGTTGCTTAACACCAGCCGCCATATGGTTAAAGGCACGGGTAACGGAACGCACCTCCGAAGCGCCATACTCACGCAGCGGCGGCGGAATAATCCCTTTACCa  <  1:107463/275‑1 (MQ=255)                                                                                                                                                                                                                                                        gTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTAc                                                                                                                                       >  1:212639/1‑138 (MQ=255)                                                                                                                                                                                                                                                        gTCGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTACCCCCGCCATCAGCAGCGTGCGGTCATCCGCCAGTTGCTTa                                                                                               >  2:111119/1‑178 (MQ=255)                                                                                                                                                                                                                                                          cGATACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTAcccc                                                                                                                                    >  1:57286/1‑139 (MQ=255)                                                                                                                                                                                                                                                            aTACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTAccccc                                                                                                                                   <  2:212637/138‑1 (MQ=255)                                                                                                                                                                                                                                                            aTACACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTACCCCCGCCATCAGCAGCGTGCGGTCATCCGCCAGTTGCTTAacac                                                                                           <  1:111119/178‑1 (MQ=255)                                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                                        ACCAGGCGCGATTCGGCTCCGTTCCGCTGCTGACTTTGATCCAGCCATTGCCATAACGGGCGGCGTTGACCACCATATTCGCCACCGCGCGTTTGATCGACAGCGGGTGCATTTTCACTTCAATGCTGCCGGGGTAAAGCGCGGTTTCAATTTCCCGCTCATAGCCACTTTCGGCAGCAATCACCTCACCGAGTACTGCATTAAGATCCGCCATTTCCATCGGCATCTCCTGCCCGGTGCGCAGGTAGTCGATAAACTGCTCAATGATGGCGTTGCACTCTTCGATATCTTTATTGATCGATTCTGCCAGATAGCCATCCTGCTCGCTCATCATCTCAGTCGCCAGGCGAATACGCGTCAGCGGCGTGCGCAAGTCGTGACTTACCCCCGCCATCAGCAGCGTGCGGTCATCCGCCAGTTGCTTAACACCAGCCGCCATATGGTTAAAGGCACGGGTAACGGAACGCACCTCCGAAGCGCCATACTCACGCAGCGGCGGCGGAATAATCCCTTTACCA  >  CP009273/3528123‑3528640

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑