Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,928,022	C→T	11.3%	G717D (GGC→GAC)	cheA ←	chemotaxis histidine kinase CheA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,928,022	0	C	T	11.3%	139.9 / 7.8	53	G717D (GGC→GAC)	cheA	chemotaxis histidine kinase CheA
Reads supporting (aligned to +/- strand):  ref base C (20/27);  new base T (2/4);  total (22/31)
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

TGCCATAAACACTCCATTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTGCCGACCGACAGAATCACCACGTGGCCCTCGTGCTGCTCTTCGTGCACCTG  >  NC_002947/4927876‑4928164                                                                                                                                                    |                                                                                                                                                tGCCATAAACACTCCATTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTGGCCGGTAATGGTGGCCACGGACATGccc                                                                                                                                               >  7:142447/1‑149 (MQ=255)    cATAAACACTCCATTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCggg                                                                                                                                            <  5:65233/149‑1 (MQ=255)       aaaCACTCCATTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGGCATGTCCggggcc                                                                                                                                         <  5:42567/149‑3 (MQ=255)        aaCCCTCCATTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGGCATGTCCggggcc                                                                                                                                         <  8:62453/148‑3 (MQ=255)        aaCACTCCATTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGc                                                                                                                                        <  5:346223/149‑1 (MQ=255)        aaCACTCCATTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGGGGCCCCGGGCATGTCCggggcca                                                                                                                                        <  3:7115/149‑4 (MQ=255)             tCCATTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTg                                                                                                                                    >  6:173073/1‑148 (MQ=255)               cATTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTgcag                                                                                                                                 >  5:215061/1‑149 (MQ=255)                aTTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGGCATGTCCgggg                                                                                                                                           <  3:82258/138‑1 (MQ=255)                aTTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGGCATGTCCgggg                                                                                                                                           >  4:82258/1‑138 (MQ=255)                    ggcggcGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATc                                                                                                                             <  6:215061/148‑1 (MQ=255)                     gcggcgCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCtt                                                                                                                                     >  1:25761/1‑139 (MQ=255)                     gcggcgCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCtt                                                                                                                                     <  2:25761/139‑1 (MQ=255)                       ggcgCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGc                                                                                                                         >  4:245242/1‑149 (MQ=255)                             aCCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTACCCAGCg                                                                                                                   <  4:315406/149‑1 (MQ=255)                                     gggCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCTCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTtgatg                                                                                                           >  3:12678/1‑149 (MQ=255)                                      ggCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTtgatga                                                                                                          <  2:164887/149‑1 (MQ=255)                                       gcgcgcCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCt                                                                                                                <  4:58498/142‑1 (MQ=255)                                       gcgcgcCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCt                                                                                                                >  3:58498/1‑142 (MQ=255)                                       gcgcgcCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTtgatga                                                                                                          <  5:70173/148‑1 (MQ=255)                                        cgcgcCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGAcc                                                                                                        <  3:245242/149‑1 (MQ=255)                                         gcgcCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCa                                                                                                       <  2:328003/149‑1 (MQ=255)                                                cGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCgg                                                                                                                                             >  7:20831/1‑104 (MQ=255)                                                cGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCgg                                                                                                                                             <  8:20831/104‑1 (MQ=255)                                                       aaaTACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCTCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGccc                                                                                         <  4:12678/149‑1 (MQ=255)                                                         aTACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCtt                                                                                                               >  8:199492/1‑125 (MQ=255)                                                         aTACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCtt                                                                                                               <  7:199492/125‑1 (MQ=255)                                                          tACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGAGCGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCccac                                                                                       >  1:247613/1‑149 (MQ=255)                                                             gccgcGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGt                                                                                   >  5:80185/1‑149 (MQ=255)                                                             gccgcGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGt                                                                                   <  6:59212/149‑1 (MQ=255)                                                               cgcgcgGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTg                                                                                 <  2:247613/149‑1 (MQ=255)                                                                     gcgTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTcgac                                                                           <  6:238886/149‑1 (MQ=255)                                                                         aaCGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTgca                                                                                                                                  <  1:11815/90‑1 (MQ=255)                                                                         aaCGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTgca                                                                                                                                  >  2:11815/1‑90 (MQ=255)                                                                         aaCGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCccac                                                                                       <  5:108974/133‑1 (MQ=255)                                                                         aaCGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCccac                                                                                       >  6:108974/1‑133 (MQ=255)                                                                          aCGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACaa                                                                      <  6:80185/149‑1 (MQ=255)                                                                            gCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACaaaa                                                                    <  3:2109/149‑1 (MQ=255)                                                                                gAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGa                                                                >  2:291959/1‑149 (MQ=255)                                                                                        tCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTgg                                                       >  8:38848/1‑149 (MQ=255)                                                                                           ggA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTg                                                    >  4:324203/1‑149 (MQ=255)                                                                                            gA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTGc                                                   >  6:190398/1‑149 (MQ=255)                                                                                                 tcgccactCACCGCGACGCGACCGTCGCCCGTAAAGCGGGCCCCCCACCCGCCCGGGGGGCCTTGCAGCACCTTGCCCCCCGGCGTGCAGACCACTTCTTCCAGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTGccgac                                               <  8:345687/142‑1 (MQ=255)                                                                                                 tCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTGccgac                                               <  5:173073/149‑1 (MQ=255)                                                                                                           aCGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTGCCGACCGACAGAAt                                      >  6:171769/1‑148 (MQ=255)                                                                                                              cgATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTGCCGACCGACAGAATcacc                                  <  3:324203/149‑1 (MQ=255)                                                                                                                 tGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTGCCGACCGACAGAATCACCACg                               >  2:198950/1‑149 (MQ=255)                                                                                                                     aCCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGAAGC‑GCTGGGTGCCGACCGACAGAATCACAACGTgga                           >  8:72232/1‑148 (MQ=255)                                                                                                                           gCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTGCCGACCGACAGAATCACCACGTGGCCCTCg                      <  1:198950/148‑1 (MQ=255)                                                                                                                            ccGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTg                                                                                 <  4:35755/89‑1 (MQ=255)                                                                                                                            ccGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTg                                                                                 >  3:35755/1‑89 (MQ=255)                                                                                                                                      gcaccccGGGCATGTCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACATCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTGCCGACCGACAGAATCACCACGTGGCCCTCGTGCTGCTCTTCg          >  8:321761/4‑149 (MQ=255)                                                                                                                                              gACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTGCCGACCGACAGAATCACCACGTGGCCCTCGTGCTGCTCTTCGTGCACCTg  <  7:38848/149‑1 (MQ=255)                                                                                                                                               aCATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGCTGCTGGGTGCCGACCGACAGAATCACCACGTGGCCCTCGTGCTGCTCTTCGTGCACCTg  <  1:291959/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                TGCCATAAACACTCCATTAGGCGGCGCAACCCGCCAGGGCGCGCCACCGAAATCAAATACGCCGCGCGGCGTAACGCTTGAGCATGCTCGGGA‑CGTCGAGAATCAACGCGATGCGACCGTCGCCGGTAATGGTGGCCCCGGACATGCCCGGGGTGCCTTGCAGCATCTTGCCCAGCGGCTTGATGACCACTTCTTCCTGGCCCACCAGTTGGTCGACGACAAAACCGATGC‑GCTGGGTGCCGACCGACAGAATCACCACGTGGCCCTCGTGCTGCTCTTCGTGCACCTG  >  NC_002947/4927876‑4928164

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: ‑