Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,970,004	C→A	11.0%	G80V (GGC→GTC)	fliC ←	flagellin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,970,004	0	C	A	11.0%	159.5 / 9.7	55	G80V (GGC→GTC)	fliC	flagellin
Reads supporting (aligned to +/- strand):  ref base C (26/22);  new base A (4/2);  total (31/24)
Fisher's exact test for biased strand distribution p-value = 6.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.46e-01

AGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGCCAGAGGA  >  NC_002947/4969862‑4970146                                                                                                                                                |                                                                                                                                               aGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTca                                                                                                                                           <  6:99456/148‑1 (MQ=255)           gTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTgcg                                                                                                                                 >  2:180275/1‑148 (MQ=255)               gCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATa                                                                                                                            <  6:299180/149‑1 (MQ=255)                 tCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATa                                                                                                                            >  5:354442/1‑147 (MQ=255)                   gCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCACCGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATagag                                                                                                                         <  1:289809/149‑1 (MQ=255)                   gCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTcagca                                                                                                                                        <  4:65241/133‑1 (MQ=255)                   gCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTcagca                                                                                                                                        >  3:65241/1‑133 (MQ=255)                     ccGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTAGAGCCGTACGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGACTGAAGTCTCCATCGCGCCTTCAGCAGTTTGCGCAATAGAGAt                                                                                                                       >  8:75629/1‑148 (MQ=255)                                     cTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCt                                                                                                      <  5:64388/149‑1 (MQ=255)                                      tCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGAGTGAAGGGCCAGTTCA‑CGCATACGGTGCATGATGTTGCCTGAAGTCGCGATGGCGCCTTCTGCAGTTGGCGGAAGAGAGCTACCCTCGTTGGctggctt                                                                                                     >  8:147088/1‑143 (MQ=255)                                         tgctgcATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGAc                                                                                                  >  8:181092/1‑149 (MQ=255)                                           ctgcATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGAc                                                                                                  <  4:209346/147‑1 (MQ=255)                                           ctgcATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGAc                                                                                                  <  2:302630/147‑1 (MQ=255)                                                 ggAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGc                                                                                          >  2:41926/1‑149 (MQ=255)                                                          gtcgtcATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtt                                                                                 >  1:213965/1‑149 (MQ=255)                                                          gtcgtcATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtt                                                                                 <  1:41926/149‑1 (MQ=255)                                                           tcgtcATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGtt                                                                                                              >  2:80627/1‑119 (MQ=255)                                                           tcgtcATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGtt                                                                                                              <  1:80627/119‑1 (MQ=255)                                                                 tCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtttgattt                                                                           >  8:72218/1‑148 (MQ=255)                                                                 tCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtt                                                                                 <  6:360316/142‑1 (MQ=255)                                                                 tCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtt                                                                                 >  5:360316/1‑142 (MQ=255)                                                                   gCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtttgatttga                                                                         <  7:181092/148‑1 (MQ=255)                                                                   gCTGTTCGACCCGTTCGCCGATTGCAGGGCCAGTTCA‑AGCATACGCTGCATGATGTTGGCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCTCTACGCTCAGACCTTTGATTTGAg                                                                        <  7:75629/149‑1 (MQ=255)                                                                             ccGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtt                                                                                 <  3:265938/130‑1 (MQ=255)                                                                             ccGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCtt                                                                                 >  4:265938/1‑130 (MQ=255)                                                                                ttCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGtt                                                           <  5:178578/149‑1 (MQ=255)                                                                                   gCCGATTGCATTGCCAGTTCA‑CTCATACGATTCATGATGTTGCCTGAAGTCGCCATGGCGACtt                                                                                                                                             <  6:97170/64‑1 (MQ=255)                                                                                   gCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGGCATGGCGGCTTCACGAGTTTTCGGAATAGCGTAACCATCGTTGGGGTTGTTGGCCCCACCGGTCAGCCCTTTGATTTGAGTGGTCAGGCGGTTg                                                          >  2:159597/1‑147 (MQ=255)                                                                                   gCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTgg                                                         <  2:213965/148‑1 (MQ=255)                                                                                   gCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGGCGCCATGGCGACtt                                                                                                                                             >  5:97170/1‑64 (MQ=255)                                                                                       aTTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATc                                                    >  3:33534/1‑149 (MQ=255)                                                                                       aTTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTGTGATTTGAGTGGTCAGACGGTTg                                                          >  4:67006/1‑143 (MQ=255)                                                                                           cAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGc                                                 <  7:72218/148‑1 (MQ=255)                                                                                            aGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAg                                               <  6:354442/149‑1 (MQ=255)                                                                                                   gTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTgcg                                        >  8:45698/1‑149 (MQ=255)                                                                                                       a‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGcgt                                    >  3:67919/1‑149 (MQ=255)                                                                                                            aTACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGa                                                                                                   <  6:39664/82‑1 (MQ=255)                                                                                                            aTACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGa                                                                                                   >  5:39664/1‑82 (MQ=255)                                                                                                                gCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTg                            <  1:180275/149‑1 (MQ=255)                                                                                                                    cATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGTCCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCAc                        >  1:244600/1‑149 (MQ=255)                                                                                                                           ttGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGa                  <  5:279557/148‑1 (MQ=255)                                                                                                                            tGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGAtt                >  2:16489/1‑149 (MQ=255)                                                                                                                               cTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGAtttt              >  1:156886/1‑148 (MQ=255)                                                                                                                               cTGAAGGCGCCATGGCGACTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGAtttt              >  2:139820/1‑148 (MQ=255)                                                                                                                               cTGAAGGCGCCATGGCGACTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGAtttt              >  2:200634/1‑148 (MQ=255)                                                                                                                                tGAAGGCGCCATGGCGACTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGAtttt              >  3:344199/1‑147 (MQ=255)                                                                                                                                 gAAGTCGCCATGGCGCCTTCAGCAGATTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCAGCGGCTTCGTCTTTGGCACTGTTGATTTTCAg           >  6:169580/1‑149 (MQ=255)                                                                                                                                  caggcGCCCTGGCGACTTCAGCTGTTTGCGCAATAGACATACCATCGTTGCCGTTCTTGACCGCAACGCTCAGAGCTTTGATTTGAGTGGTCTGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCa            <  4:344199/143‑1 (MQ=255)                                                                                                                                  aaGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAg           <  4:33534/148‑1 (MQ=255)                                                                                                                                       gCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGCCaga     <  7:45698/149‑1 (MQ=255)                                                                                                                                       gCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGCCa       >  1:284006/1‑147 (MQ=255)                                                                                                                                        ccATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGCCagag    >  8:223724/1‑149 (MQ=255)                                                                                                                                         cATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGCCagag    >  3:92191/1‑148 (MQ=255)                                                                                                                                          aTGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGCCAGAGGa  >  7:107221/1‑149 (MQ=255)                                                                                                                                           tGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGCCAGAGGa  >  3:279168/1‑148 (MQ=255)                                                                                                                                             gcgcCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGCCAGAGGa  >  6:62986/1‑146 (MQ=255)                                                                                                                                                |                                                                                                                                               AGCAATACGGGTGAGCTCGCCCGACAGCGCGGTAAACTCCTGCTGCATGGAGGCGCGGTCGTCATCGCTGTTCGAGCCGTTCGCCGATTGCAGGGCCAGTTCA‑CGCATACGCTGCATGATGTTGCCTGAAGTCGCCATGGCGCCTTCAGCAGTTTGCGCAATAGAGATACCATCGTTGGCGTTCTTGACCGCAACGCTCAGACCTTTGATTTGAGTGGTCAGACGGTTGGAGATCTGCAGGCCTGCGGCGTCGTCTTTGGCACTGTTGATTTTCAGGCCAGAGGA  >  NC_002947/4969862‑4970146

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑