Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,979,209	T→A	6.7%	intergenic (‑37/‑203)	PP_5241 ← / → PP_5242	LuxR family transcriptional regulator/GAF domain‑containing sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,979,209	0	T	A	6.7%	184.8 / 4.6	60	intergenic (‑37/‑203)	PP_5241/PP_5242	LuxR family transcriptional regulator/GAF domain‑containing sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base T (26/30);  new base A (2/2);  total (28/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.90e-01

TCAGCGTGGCCAGCACGTCGAAAGCACGCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACGGACAACAGCGTGCCCGTTCCTGCCAAGCAGGCTGTAACCCGCATCCAT  >  NC_002947/5979064‑5979357                                                                                                                                                  |                                                                                                                                                     tCAGCGTGGCCAGCACGTCGAAAGCACGCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGc                                                                                                                                                  <  1:589899/150‑1 (MQ=255)  cAGCGTGGCCAGCACGTCGAAAGCACGCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCa                                                                                                                                                 >  1:701557/1‑150 (MQ=255)       tGGCCAGCACGTCGAAAGCACGCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCAGGGCAGcgaa                                                                                                                                            <  1:70621/150‑4 (MQ=255)        ggCCAGCACGTCGAAAGCACGCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCATAg                                                                                                                                           >  1:678373/1‑150 (MQ=255)                 gTCGAAAGCACGCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGtt                                                                                                                                  >  1:208449/1‑150 (MQ=255)                    gAAAGCACGCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGGCTATTCGGATCATGGCTTCCTCGCGCGGGCACCGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGc                                                                                                                               <  1:716842/150‑1 (MQ=255)                    gAAAGCACGCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCAAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGc                                                                                                                               <  1:407468/150‑1 (MQ=255)                            gCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGAc                                                                                                                       >  2:446297/1‑150 (MQ=255)                            gCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCAGGGCAGc                                                                                                                                               <  1:18950/126‑1 (MQ=255)                            gCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCAGGGCAGc                                                                                                                                               >  2:18950/1‑126 (MQ=255)                              ccacccaACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACaa                                                                                                                     >  2:337617/1‑150 (MQ=255)                               cacccaACAGGCTCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAAt                                                                                                                    >  1:192345/1‑150 (MQ=255)                                acccaACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGtt                                                                                                                                  <  2:521172/135‑1 (MQ=255)                                acccaACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGtt                                                                                                                                  >  1:521172/1‑135 (MQ=255)                                        ggATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAg                                                                                                           <  1:684658/150‑1 (MQ=255)                                         gATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGa                                                                                                            >  1:355614/1‑148 (MQ=255)                                         gATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGa                                                                                                            <  2:355614/148‑1 (MQ=255)                                         gATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAgg                                                                                                          <  1:446297/150‑1 (MQ=255)                                                    cGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGc                                                                                               <  1:542244/150‑1 (MQ=255)                                                    cGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGc                                                                                               <  2:701557/150‑1 (MQ=255)                                                    cGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGAGTTCACACAATTATCCCGAGGGATAGGTTGGc                                                                                               <  1:743709/150‑1 (MQ=255)                                                    cGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCAAGGGCGTTTTCGCTGCCCTGGTGTTCCGAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGc                                                                                               <  1:337617/150‑1 (MQ=255)                                                     gTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAg                                                                                                                                           <  2:595089/105‑1 (MQ=255)                                                     gTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAg                                                                                                                                           >  1:595089/1‑105 (MQ=255)                                                           aaaGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCaa                                                                                           >  2:65572/1‑147 (MQ=255)                                                           aaaGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCaa                                                                                           <  1:65572/147‑1 (MQ=255)                                                                 ttCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGa                                                                                                                        >  1:203977/1‑112 (MQ=255)                                                                 ttCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGa                                                                                                                        <  1:258775/112‑1 (MQ=255)                                                                 ttCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGa                                                                                                                        >  2:258775/1‑112 (MQ=255)                                                                 ttCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGa                                                                                                                        <  2:203977/112‑1 (MQ=255)                                                                 ttCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCATAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATAc                                                                                  <  2:678373/150‑1 (MQ=255)                                                                       ccgcTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGc                                                                            <  1:442239/150‑1 (MQ=255)                                                                                      cTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGc                                                                                                                                               <  2:759474/68‑1 (MQ=255)                                                                                      cTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGc                                                                                                                                               >  1:759474/1‑68 (MQ=255)                                                                                             ttGCCTATTCGGATAATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGAt                                                                                                       >  2:185036/1‑101 (MQ=255)                                                                                             ttGCCTATTCGGATAATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGAt                                                                                                       <  1:185036/101‑1 (MQ=255)                                                                                                ccTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCATACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGccc                                                                  >  2:425411/1‑135 (MQ=255)                                                                                                ccTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGccc                                                                  <  1:425411/135‑1 (MQ=255)                                                                                                 cTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACg                                                  <  1:370333/150‑1 (MQ=255)                                                                                                        gATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGc                                                                        >  1:436597/1‑121 (MQ=255)                                                                                                        gATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGc                                                                        <  2:436597/121‑1 (MQ=255)                                                                                                         aTCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACGATACAAAAGCCCGCGGTCCCCTAGGGGACGATAACGGACAACAg                                          >  2:528861/1‑150 (MQ=255)                                                                                                             tGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGttt                                                                                                 >  1:434634/1‑90 (MQ=255)                                                                                                             tGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGttt                                                                                                 <  2:434634/91‑2 (MQ=255)                                                                                                               gCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACGGACAACAGCGTGcc                                    >  2:462437/1‑150 (MQ=255)                                                                                                                    cTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACGGACAACAGCGTGCCCGTTc                               <  2:192345/150‑1 (MQ=255)                                                                                                                    cTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACGGACAACAGCGTGCCCGTTc                               >  2:719105/1‑150 (MQ=255)                                                                                                                       gcgcgGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAAc                                                   >  2:715670/1‑127 (MQ=255)                                                                                                                       gcgcgGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAAc                                                   <  1:715670/127‑1 (MQ=255)                                                                                                                               aCGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACGGACAACAGCGTGCCCGTTCCTGCCAAGCAg                    <  1:780768/150‑1 (MQ=255)                                                                                                                                 gggCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCa                                                                                                                          <  1:679854/46‑1 (MQ=255)                                                                                                                                 gggCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCa                                                                                                                          >  2:679854/1‑46 (MQ=255)                                                                                                                                 gggCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAAGCCGATACAAAAGCCCGCCTGCCGCAAGGGGACGATAACGGACAACAGCGTGCGTGTTCCGGCTAAGCAGGc                  >  1:336846/1‑150 (MQ=255)                                                                                                                                   gCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACGGacaaca                                           <  2:627019/123‑1 (MQ=255)                                                                                                                                   gCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACGGacaaca                                           >  1:627019/1‑123 (MQ=255)                                                                                                                                       caacGCTGGCCTAGGCTGCCCAGGGCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACtat                                                                                    <  2:600809/75‑1 (MQ=21)                                                                                                                                       caacGCTGGCCTAGGCTGCCCAGGGCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACtat                                                                                    >  1:600809/4‑78 (MQ=21)                                                                                                                                          ggCTGCCCAGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACGGACAACAGCGTGCCCGTTCCTGCCAAGCAGGCTGTAACCCg         >  2:411811/2‑150 (MQ=255)                                                                                                                                             tGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACGGACAACAGCGTGCCCGTTCCTGCCAAGCAGGCTGTAACCCGCAt      >  1:186927/1‑150 (MQ=255)                                                                                                                                                 cTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACGGACAACAGCGTGCCCGTTCCTGCCAAGCAGGCTGTAACCCGCATCCAt  <  1:528861/150‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                     TCAGCGTGGCCAGCACGTCGAAAGCACGCCCACCCAACAGGATCGGCTTGCCGTCGACAAAGACTTCGCGCCGCTCCAGCGACACCTGGGCATTGCCTATTCGGATCATGGCTTCCTCGCGCGGGCACGGGCGTTTTCGCTGCCCTGGGCAGCCTAGGCCAGCGTTGGCGTTCAGACAATTATCCCGAGGGATAGGTTGGCCCAAGGACTATACAAAAGCCCGCCTGCCCCAAGGGGACGATAACGGACAACAGCGTGCCCGTTCCTGCCAAGCAGGCTGTAACCCGCATCCAT  >  NC_002947/5979064‑5979357

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑