Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,284,338	T→G	8.8%	G92G (GGT→GGG)	PP_1121 →	OmpA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,284,338	0	T	G	8.8%	129.5 / 2.3	45	G92G (GGT→GGG)	PP_1121	OmpA family protein
Reads supporting (aligned to +/- strand):  ref base T (18/23);  new base G (2/2);  total (20/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

GCCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACAAAGAGCGCCTC  >  NC_002947/1284192‑1284485                                                                                                                                                    |                                                                                                                                                    gcCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGgtgt                                                                                                                                                   <  2:195926/149‑1 (MQ=255) gcCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CACCACGCGgggt                                                                                                                                                   <  7:67057/149‑1 (MQ=255)    aTCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGtgtg                                                                                                                                                  >  3:157498/1‑147 (MQ=255)       gAAAGCTCCAGCTGGGCTGTCTGGGTTGCGTTGCTGGGCGGTGGCGTGGCGGCGGGATATTGCTGGGCCCATGGCGATGTCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGt                                                                                                                                             <  4:109892/149‑1 (MQ=255)                          gctggGGTGCGTTGCTGGGCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCg                                                                                                                          >  1:110298/1‑149 (MQ=255)                              gggTGCGTTGCTGGGCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCt                                                                                                                       >  2:178986/1‑148 (MQ=255)                                gTGCGTTGCTGGGCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAg                                                                                                                    >  6:179873/1‑149 (MQ=255)                                    gTTGCTGGGCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCACCCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCg                                                                                                                 <  1:240067/149‑1 (MQ=255)                                       gCTGGGCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGtt                                                                                                              <  2:110298/148‑1 (MQ=255)                                         tGGGCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCg                                                                                                           >  3:329198/1‑149 (MQ=255)                                           ggCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCggt                                                                                                         <  2:284552/149‑1 (MQ=255)                                           ggCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCggt                                                                                                         <  8:159818/149‑1 (MQ=255)                                           ggCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCggt                                                                                                         <  4:253304/149‑1 (MQ=255)                                            gCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCggtg                                                                                                        <  6:277268/149‑1 (MQ=255)                                              ggTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCAGTGACACGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCggtggt                                                                                                      <  8:274765/149‑1 (MQ=255)                                                   ccTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCgaag                                                                                                 <  8:90937/149‑1 (MQ=255)                                                   ccTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑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                                                                                       >  7:270550/1‑149 (MQ=255)                                                             ggCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAgtggtggt                                                                                       <  2:145189/149‑1 (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                                                                                         >  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                   <  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)                                                                                                                                                gtggtgTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACAAAGAgcgc     >  4:321035/1‑149 (MQ=255)                                                                                                                                                   gtgtGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACaaa           >  2:88003/1‑140 (MQ=255)                                                                                                                                                   gtgtGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACaaa           <  1:88003/140‑1 (MQ=255)                                                                                                                                                    tgtgCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACAAAGAGCGCCTc  >  4:193818/1‑148 (MQ=255)                                                                                                                                                    |                                                                                                                                                    GCCATCGAAAGCTCCAGCTGGGCTGGCTGGGGTGCGTTGCTGGGCGGTGGCCTGGCGGCGGGCTATTGCTGGGCCCATGGCGATGGCGACGAGGATGGTGACGGCGTGCCAGACAGCCGTGACAAGTGCCCTGGCA‑CCCCGCGTGGTGTGCAGGTCGATGCCAACGGATGCCCGCCTGAGCCGGTTGCGGTGGTCGAAGAAGTGGTGGTGCAGAAGGAAGAAGTCATTGTCATCCGCGATGTGCACTTCGAGTTCGATTCTGCGCGCCTGACGGCCAGTGACAAAGAGCGCCTC  >  NC_002947/1284192‑1284485

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: ‑