Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,284,332	G→A	10.0%	P90P (CCG→CCA)	PP_1121 →	OmpA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,284,332	0	G	A	10.0%	133.4 / 5.3	50	P90P (CCG→CCA)	PP_1121	OmpA family protein
Reads supporting (aligned to +/- strand):  ref base G (19/26);  new base A (2/3);  total (21/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

TGGGCGCCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACAAAGAG  >  NC_002947/1284187‑1284479                                                                                                                                                       |                                                                                                                                                    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                                                                                                   <  8:159818/149‑1 (MQ=255)                                                ggCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCggt                                                                                                   <  2:284552/149‑1 (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                                                                                           <  8:90937/149‑1 (MQ=255)                                                        ccTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCgaag                                                                                           <  7:151530/149‑1 (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                                                  <  5:199859/135‑1 (MQ=255)                                                                                                                   gTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGAt                                                  >  6:199859/1‑135 (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                                                                                   <  2:146817/82‑1 (MQ=255)                                                                                                                                       gTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAgtggtg                                                                                   >  1:146817/1‑82 (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             <  6:268585/144‑1 (MQ=255)                                                                                                                                             ctgCA‑CACCACGCGGGGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCa             >  5:268585/3‑146 (MQ=255)                                                                                                                                                 a‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACa       >  6:156050/1‑148 (MQ=255)                                                                                                                                                 a‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGCGACa       >  7:28300/1‑148 (MQ=255)                                                                                                                                                     ccGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACaaa     >  8:103954/1‑147 (MQ=255)                                                                                                                                                      cgcgTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACAAagag  >  4:129144/1‑149 (MQ=255)                                                                                                                                                       |                                                                                                                                                    TGGGCGCCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTG‑GC‑‑GG‑CGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACAAAGAG  >  NC_002947/1284187‑1284479

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: ‑