Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,284,329	C→A	10.2%	T89T (ACC→ACA)	PP_1121 →	OmpA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,284,329	0	C	A	10.2%	143.8 / 5.6	49	T89T (ACC→ACA)	PP_1121	OmpA family protein
Reads supporting (aligned to +/- strand):  ref base C (18/26);  new base A (2/3);  total (20/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

CGCCCTGGGCGCCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACA  >  NC_002947/1284182‑1284474                                                                                                                                                         |                                                                                                                                                  cgccCTGGGCGCCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑ccc                                                                                                                                                  <  5:35192/149‑1 (MQ=255)  gccCTGGGCGCCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑cccc                                                                                                                                                 >  7:90937/1‑149 (MQ=255)      tGGGCGCCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCgt                                                                                                                                             >  5:277268/1‑149 (MQ=255)        ggCGCCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCgtg                                                                                                                                            <  1:229313/148‑1 (MQ=255)           gcCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTGCGCAGGGCCCGGCCCCCCTTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCgtg                                                                                                                                            <  1:111845/149‑1 (MQ=255)           gcCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGgtgt                                                                                                                                        <  2:195926/149‑1 (MQ=255)           gcCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CACCACGCGgggt                                                                                                                                        <  7:67057/149‑1 (MQ=255)              aTCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGtgtg                                                                                                                                       >  3:157498/1‑147 (MQ=255)                 gAAAGCTCCAGCTGGGCTGTCTGGGTTGCGTTGCTGGGCGGTGGCGTG‑GC‑‑GG‑CGGGATATTGCTGGGCCCATGGCGATGTCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGt                                                                                                                                  <  4:109892/149‑1 (MQ=255)                                    gctggGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCg                                                                                                               >  1:110298/1‑149 (MQ=255)                                        gggTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCt                                                                                                            >  2:178986/1‑148 (MQ=255)                                          gTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAg                                                                                                         >  6:179873/1‑149 (MQ=255)                                              gTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCACCCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCg                                                                                                      <  1:240067/149‑1 (MQ=255)                                                 gCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGtt                                                                                                   <  2:110298/148‑1 (MQ=255)                                                   tGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCg                                                                                                >  3:329198/1‑149 (MQ=255)                                                     ggCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCggt                                                                                              <  2:284552/149‑1 (MQ=255)                                                     ggCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCggt                                                                                              <  8:159818/149‑1 (MQ=255)                                                     ggCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCggt                                                                                              <  4:253304/149‑1 (MQ=255)                                                      gCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCggtg                                                                                             <  6:277268/149‑1 (MQ=255)                                                        ggTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCAGTGACACGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCggtggt                                                                                           <  8:274765/149‑1 (MQ=255)                                                             ccTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCgaag                                                                                      <  7:151530/149‑1 (MQ=255)                                                             ccTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCgaag                                                                                      <  8:90937/149‑1 (MQ=255)                                                                         cggGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAgtggtg                                                                              <  4:329198/149‑1 (MQ=255)                                                                          gggCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAgtggtgg                                                                             <  8:34698/149‑1 (MQ=255)                                                                           ggCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAgtggtggt                                                                            <  2:145189/149‑1 (MQ=255)                                                                           ggCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAgtggtggt                                                                            >  7:270550/1‑149 (MQ=255)                                                                            gCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAgtggtggtg                                                                           >  6:50947/1‑149 (MQ=255)                                                                                  gCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAgaag                                                                     >  1:129718/1‑149 (MQ=255)                                                                                     gggCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGATCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAgaaggaa                                                                  >  3:221431/1‑149 (MQ=255)                                                                                        cccATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGgaagaa                                                               <  8:270550/149‑1 (MQ=255)                                                                                           atggcgatggcgACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGt                                                             >  7:94743/1‑148 (MQ=255)                                                                                               cgatggcgaCGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTg                                                        <  5:179215/149‑1 (MQ=255)                                                                                                                        gTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGAt                                             >  6:199859/1‑135 (MQ=255)                                                                                                                        gTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGAt                                             <  5:199859/135‑1 (MQ=255)                                                                                                                        gTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGtt                               <  1:178986/149‑1 (MQ=255)                                                                                                                           ccAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGa                            <  5:50947/149‑1 (MQ=255)                                                                                                                              gACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTc                         >  5:108336/1‑149 (MQ=255)                                                                                                                               aCAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCt                        <  5:179873/149‑1 (MQ=255)                                                                                                                                   ccGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTgcgc                    >  5:108920/1‑149 (MQ=255)                                                                                                                                          aaGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGAc             <  4:157498/149‑1 (MQ=255)                                                                                                                                            gTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAgtggtg                                                                              >  1:146817/1‑82 (MQ=255)                                                                                                                                            gTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAgtggtg                                                                              <  2:146817/82‑1 (MQ=255)                                                                                                                                              gCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGc          >  6:16420/1‑148 (MQ=255)                                                                                                                                                ccTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAg       <  5:16420/149‑1 (MQ=255)                                                                                                                                                 cctgCA‑CACCACGCGGGGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGa                            >  6:216275/4‑127 (MQ=255)                                                                                                                                                 cctgCA‑CACCACGCGGGGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGa                            <  5:216275/124‑1 (MQ=255)                                                                                                                                                 cTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGt      <  8:94743/149‑1 (MQ=255)                                                                                                                                                  ctgCA‑CACCACGCGGGGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCa        >  5:268585/3‑146 (MQ=255)                                                                                                                                                  ctgCA‑CACCACGCGGGGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCa        <  6:268585/144‑1 (MQ=255)                                                                                                                                                      a‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACa  >  6:156050/1‑148 (MQ=255)                                                                                                                                                      a‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGCGACa  >  7:28300/1‑148 (MQ=255)                                                                                                                                                         |                                                                                                                                                  CGCCCTGGGCGCCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACA  >  NC_002947/1284182‑1284474

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: ‑