Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,377,695	C→A	6.9%	L258M (CTG→ATG)	tnpB →	transposase subunit B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,377,695	0	C	A	6.9%	180.7 / 2.6	58	L258M (CTG→ATG)	tnpB	transposase subunit B
Reads supporting (aligned to +/- strand):  ref base C (24/30);  new base A (2/2);  total (26/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.24e-01

TACAGCGAGCGGCTGGGCGAAGCTGGCATCGAACCCTCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCAACCATATCGGTTGCTGCCTGACTCAAACAAAACA  >  NC_002947/3377548‑3377842                                                                                                                                                     |                                                                                                                                                    tACAGCGAGCGGCTGGGCGAAGCTGGCATCGAACCCTCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTg                                                                                                                                                   <  2:840680/150‑1 (MQ=255)   cAGCGAGCGGCTGGGCGAAGCTGGCATCGAACCCTCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGa                                                                                                                                                 <  2:732757/150‑1 (MQ=255)              tGGGCGAAGCTGGCATCGAACCCTCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGc                                                                                                                                      >  1:273854/1‑150 (MQ=255)                     aGCTGGCATCGAACCCTCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTg                                                                                                                               <  1:253349/150‑1 (MQ=255)                      gCTGGCATCGAACCCTCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTgg                                                                                                                              <  1:906464/150‑1 (MQ=255)                      gCTGGCATCGAACCCTCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTATGGAGTGGGAAACGCTGAAGTgg                                                                                                                              >  1:201452/1‑150 (MQ=255)                      ccTGGCCTCAAACCCTCGCTTTGCAATACCGGTCAACGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTgg                                                                                                                              <  1:765001/149‑1 (MQ=255)                        tGGCATCGAACCCTCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGt                                                                                                                            >  1:1062110/1‑150 (MQ=255)                         ggCATCGAACCCTCGGTTGGCAATACCGGTGACATCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACTCTGAAGTGGGTg                                                                                                                           <  1:75889/150‑1 (MQ=255)                          gCATCGAACCCTCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGCGGGCCGTGGAAAAGCGTAGACGGTCTGGAGTGGGAAACGCTGAAGTGGGTGa                                                                                                                          <  2:879718/150‑1 (MQ=255)                            accGAACCCTTGGTTGGCCATACCGGTGACAGCTACGAGAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGAcc                                                                                                                        <  2:1588589/148‑1 (MQ=255)                               gAACCCTCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTATGGAGTGGGAAACGCTGAAGTGGGTGACCTgg                                                                                                                     <  2:201452/150‑1 (MQ=255)                                     tCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAAc                                                                                                               >  2:796872/1‑150 (MQ=255)                                         ttGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATc                                                                                                           <  2:753679/150‑1 (MQ=255)                                                      tGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTATAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGa                                                                                              <  1:814366/150‑1 (MQ=255)                                                      tGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAATCATCATCGCCTGCTGGa                                                                                              <  2:808482/150‑1 (MQ=255)                                                      tGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGa                                                                                              <  2:1062110/150‑1 (MQ=255)                                                       gACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAg                                                                                             <  1:796872/150‑1 (MQ=255)                                                                   aaCGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAAt                                                                                 >  2:1057097/1‑150 (MQ=255)                                                                   aaCGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATAGGAAAt                                                                                 >  1:307171/1‑150 (MQ=255)                                                                    aCGCACTGGCAGAGACCATCAACGGCCTCTACAAGACAG‑CCTGTATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATa                                                                                <  1:15486/150‑1 (MQ=255)                                                                        aCTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGcc                                                                            >  2:1235980/1‑150 (MQ=255)                                                                         cTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCa                                                                           <  1:439814/150‑1 (MQ=255)                                                                            gCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCg                                                                        >  1:806040/1‑150 (MQ=255)                                                                                    cATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGa                                                                                              <  2:1053226/120‑1 (MQ=255)                                                                                    cATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGa                                                                                              >  1:1053226/1‑120 (MQ=255)                                                                                    cATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGtt                                                                >  2:190169/1‑150 (MQ=255)                                                                                     aTCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGttt                                                               >  2:1605363/1‑150 (MQ=255)                                                                                     aTCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGttt                                                               >  1:823071/1‑150 (MQ=255)                                                                                      tCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTggg                                                                                                                             <  2:103862/87‑1 (MQ=255)                                                                                      tCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTggg                                                                                                                             >  1:103862/1‑87 (MQ=255)                                                                                       cAACGACCTCTACAAGACCGAACTG‑CTCCATAAAGGAGGGCCGTGGAAAAGCGTAGACATTCTGGAGTAGGAAACGCTCAAGTGGGTGACCTGCTTCAACCATCAGCGCTTGCTGACTCCAATTGGAAATAAGCCACCGGCCgccccgga                                                             <  2:813693/150‑8 (MQ=255)                                                                                             ccTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGttt                                                               >  2:442796/1‑142 (MQ=255)                                                                                             ccTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGttt                                                               <  1:442796/142‑1 (MQ=255)                                                                                               tctACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACtat                                                     >  1:1353181/1‑150 (MQ=255)                                                                                                    aaGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCa                                                                           >  2:391471/1‑123 (MQ=255)                                                                                                    aaGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCa                                                                           <  1:391471/123‑1 (MQ=255)                                                                                                      gACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACa                                              >  2:877050/1‑150 (MQ=255)                                                                                                         cGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACagag                                           >  1:172889/1‑150 (MQ=255)                                                                                                         cGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACagag                                           <  1:1001865/150‑1 (MQ=255)                                                                                                               g‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGa                                                                   <  1:775344/120‑1 (MQ=255)                                                                                                               g‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGa                                                                   >  2:775344/1‑120 (MQ=255)                                                                                                                 aTCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCa                                        <  2:707942/146‑1 (MQ=255)                                                                                                                 aTCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCa                                        >  1:707942/1‑146 (MQ=255)                                                                                                                 aTCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCa                                    >  1:182765/1‑150 (MQ=255)                                                                                                                     aTAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCAACCa                                >  1:184894/1‑150 (MQ=255)                                                                                                                             gggCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCAACCATATCGGtt                        <  1:877050/150‑1 (MQ=255)                                                                                                                                 cGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGtt                                                                                                                   <  2:435588/55‑1 (MQ=255)                                                                                                                                 cGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGtt                                                                                                                   >  1:435588/1‑55 (MQ=255)                                                                                                                                     gAAAAGCGTAGACAGTATGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAg                                                                               >  1:1542479/1‑87 (MQ=255)                                                                                                                                     gAAAAGCGTAGACAGTATGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAg                                                                               <  2:1542479/87‑1 (MQ=255)                                                                                                                                            gTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCAACCATATCGGTTGCTGCCTGACTcaaa         <  2:172889/150‑1 (MQ=255)                                                                                                                                            gTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCAACCATATCGGTTGCTGCCTGACTcaaa         <  2:806040/150‑1 (MQ=255)                                                                                                                                            gTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCAACCATATCGGTTGCTGCCTGACTcaaa         <  2:1353181/150‑1 (MQ=255)                                                                                                                                                 cAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCAACCATATCggg                         >  1:1074567/1‑128 (MQ=255)                                                                                                                                                 cAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTCGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCAACCATATCggg                         <  2:1074567/129‑2 (MQ=255)                                                                                                                                                   gTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCAACCATATCGGTTGCTGCCTGACTCaaacaaaaca  >  2:12959/1‑150 (MQ=255)                                                                                                                                                   gTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCAACCATATCGGTTGCTGCCTGACTCaaacaaaaca  <  2:184894/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    TACAGCGAGCGGCTGGGCGAAGCTGGCATCGAACCCTCGGTTGGCAATACCGGTGACAGCTACGACAACGCACTGGCAGAGACCATCAACGGCCTCTACAAGACCGAACTG‑ATCCATAAGCGAGGGCCGTGGAAAAGCGTAGACAGTCTGGAGTGGGAAACGCTGAAGTGGGTGACCTGGTTCAACCATCAGCGCCTGCTGGAGCCAATTGGAAATAGGCCACCGGCCGAGTTTGAGGCACTATATGAACAGAGTCAGGCAACCATATCGGTTGCTGCCTGACTCAAACAAAACA  >  NC_002947/3377548‑3377842

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑