Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,240,105	G→C	7.1%	A62G (GCC→GGC)	PP_3717 ←	LuxR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,240,105	0	G	C	7.1%	171.2 / 3.7	56	A62G (GCC→GGC)	PP_3717	LuxR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (28/24);  new base C (2/2);  total (30/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.95e-01

CAGCAGGTAGCCGGCGCTGAAATAGCGCTCCAGCACCGCGGCCCGATGCCGTTCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATGCCCGGCAGTCTAGCCTGC  >  NC_002947/4239960‑4240251                                                                                                                                                   |                                                                                                                                                   cagcagGTAGCCGGCGCTGAAATAGCGCTCCAGCACCGCGGCCCGATGCCGTTCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCa                                                                                                                                                  <  3:66314/148‑1 (MQ=255)          gCCGGCGCTGAAATAGCGCTCCAGCACCGCGGCCCGATGCCGTTCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCcaca                                                                                                                                         <  6:136938/148‑1 (MQ=255)                      aTAGCGCTCCAGCACCGCGGCCCGATGCCGTTCGGGGATGACTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCt                                                                                                                            >  4:245090/1‑149 (MQ=255)                         gcgcTCCAGCACCGCGGCCCGATGCCGTTCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCgg                                                                                                                         <  3:245090/149‑1 (MQ=255)                         gcgcTCCAGCACCGCGGCCCGATGCCGTTCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCg                                                                                                                          <  6:23551/148‑1 (MQ=255)                                aGCACCGCGGCCCGATGCCGTTCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCCTCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACGTACTCCAGCGCCTCGGGGGTTTc                                                                                                                  <  5:171244/149‑1 (MQ=255)                                 gCACCGCGGCCCGAGCCCGTTCGGGGATGCCTGGCCGGAACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCCGACCATCCTCGACTCCACCT‑GCACCAACTGCCCGATCGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCa                                                                                                                 <  2:104872/149‑1 (MQ=255)                                       cgGCCCGATGCCGTTCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATgg                                                                                                           >  1:224407/1‑149 (MQ=255)                                            cGATGCCGTTCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACAt                                                                                                                                        <  5:293263/115‑1 (MQ=255)                                            cGATGCCGTTCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACAt                                                                                                                                        >  6:293263/1‑115 (MQ=255)                                                    ttCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGCTGCCATCGGCcagt                                                                                                                                         <  2:146480/106‑3 (MQ=255)                                                    ttCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGCTGCCATCGGCcagt                                                                                                                                         >  1:146480/1‑104 (MQ=255)                                                       ggggATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCATCATGGGCCAGGGCGCGCTGc                                                                                            <  6:352677/148‑1 (MQ=255)                                                        gggATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCaa                                                                                          >  7:182152/1‑149 (MQ=255)                                                         ggATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAAc                                                                                         <  2:224407/149‑1 (MQ=255)                                                               cTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACg                                                                                   >  2:35738/1‑149 (MQ=255)                                                                 tGCTGGTAAAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTg                                                                                 >  6:180117/1‑149 (MQ=255)                                                                      gTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCAct                                                                            >  4:66689/1‑149 (MQ=255)                                                                         cAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGCTGCCatc                                                                                                                                                <  1:264263/78‑3 (MQ=255)                                                                         cAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGCTGCCatc                                                                                                                                                >  2:264263/1‑76 (MQ=255)                                                                            cAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAg                                                                                                      >  6:134967/1‑117 (MQ=255)                                                                            cAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAg                                                                                                      <  5:134967/117‑1 (MQ=255)                                                                                  cggcgCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCTGGCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAgcgcg                                                                 >  1:267213/1‑149 (MQ=255)                                                                                      gcccgcccCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCAt                                                            >  1:141422/1‑149 (MQ=255)                                                                                            cccTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCCACGCCACGt                                                                                  >  7:304849/1‑121 (MQ=255)                                                                                                 gCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGt                                                   <  6:163663/147‑1 (MQ=255)                                                                                                 gCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGt                                                   >  5:163663/1‑147 (MQ=255)                                                                                                       aaGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCgggg                                           >  5:67615/1‑149 (MQ=255)                                                                                                       aaGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCgg                                             <  3:66689/147‑1 (MQ=255)                                                                                                        aGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCgggg                                           >  5:267792/1‑148 (MQ=255)                                                                                                               tgatcatcGACTCCAGCT‑GCACCAACTGGCGTATGGCTGCGGCCTCATACTCCAGCTCCTCGGGGGTTTCACCATGGGCGAGGTCGCGGTGCAACGCCTCGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGga                                   <  5:201149/147‑1 (MQ=255)                                                                                                                catcatcGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCgg                                     >  4:212913/1‑146 (MQ=255)                                                                                                                catcatcGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCgg                                     >  5:123640/1‑146 (MQ=255)                                                                                                                 atcatcGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGga                                   >  6:65710/1‑147 (MQ=255)                                                                                                                  tcatcGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGagag                                <  6:267792/149‑1 (MQ=255)                                                                                                                    atcGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGt                                                                                  >  2:46306/1‑97 (MQ=255)                                                                                                                    atcGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGt                                                                                  <  1:46306/97‑1 (MQ=255)                                                                                                                    atcGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGc                              >  6:243617/1‑149 (MQ=255)                                                                                                                     tcGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGTTATCGGGAGAGGcc                             <  5:180117/149‑1 (MQ=255)                                                                                                                     tcGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGcc                             >  7:102748/1‑149 (MQ=255)                                                                                                                           ccACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGTCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGt                        >  1:256995/1‑148 (MQ=255)                                                                                                                           ccACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGt                        >  7:151076/1‑148 (MQ=255)                                                                                                                             aCCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCgg                                             >  4:146667/1‑125 (MQ=255)                                                                                                                             aCCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCgg                                             <  3:146667/125‑1 (MQ=255)                                                                                                                               cT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCCCTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATGc                   >  6:54386/1‑149 (MQ=255)                                                                                                                                        aCTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATGCCCGGCAGt           >  1:56017/1‑149 (MQ=255)                                                                                                                                        aCTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATGCCCGGCAGt           <  8:151076/149‑1 (MQ=255)                                                                                                                                        aCTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATGCCCGGCAGt           <  2:56017/149‑1 (MQ=255)                                                                                                                                          tGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCAtt                                                           >  6:202596/1‑99 (MQ=255)                                                                                                                                          tGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCAtt                                                           <  5:202596/99‑1 (MQ=255)                                                                                                                                             ccGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATGCCCGGCAGTCTAGc      <  8:182152/149‑1 (MQ=255)                                                                                                                                              cGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGa                                                       <  4:351159/99‑1 (MQ=255)                                                                                                                                              cGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATGCCCGGCAGTCTAGcc     >  5:160440/1‑149 (MQ=255)                                                                                                                                               gATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATGCCCGGCAGTCTAGCCt    <  3:212913/149‑1 (MQ=255)                                                                                                                                                aTGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACTCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATTCCCGGCAg            <  5:211785/140‑1 (MQ=255)                                                                                                                                                aTGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACCCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATGCCCGGCAg            >  6:211785/1‑140 (MQ=255)                                                                                                                                                   gCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATGCCCGGCAGTCTAGCCTGc  >  1:223337/1‑147 (MQ=255)                                                                                                                                                   |                                                                                                                                                   CAGCAGGTAGCCGGCGCTGAAATAGCGCTCCAGCACCGCGGCCCGATGCCGTTCGGGGATGCCTTGCTGGTACAGCAACTGCGGCGCCCGCCCCTGGCACTCAAGGCTGATCATCATCGACTCCACCT‑GCACCAACTGGCCGATGGCAGCGGCCACATACTCCAGCGCCTCGGGGGTTTCACCATGGGCCAGGGCGCGCTGCAACGCCACGTGCCACTGCTGCAGCGCGCCCATTGTGAGGGTAAGCGGGGTATCGGGAGAGGCCTGGGTCATGCCCGGCAGTCTAGCCTGC  >  NC_002947/4239960‑4240251

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑