Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,143,646:1	+C	7.8%	coding (138/927 nt)	PP_4527 ←	DMT superfamily permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,143,646	1	.	C	7.8%	198.5 / 10.7	51	coding (138/927 nt)	PP_4527	DMT superfamily permease
Reads supporting (aligned to +/- strand):  ref base . (24/23);  new base C (2/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.97e-01

CAGTTTCAGCCCTTCGGCAATGAACAGAAACTCCACCCCGAACAGCCCGCCCGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGACCGCGCTCATAAGCGGGCCT  >  NC_002947/5143502‑5143793                                                                                                                                                  |                                                                                                                                                    cAGTTTCAGCCCTTCGGCAATGAACAGAAACTCCACCCCGAACAGCCCGCCCGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTg‑cg                                                                                                                                                   >  4:291791/1‑147 (MQ=255)        aGCCCTTCGGCAATGAACAGAAACTCCACCCCGAACAGCCCGCCCGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACTGC‑GCAATGGCATTGCCGCTGtgctg                                                                                                                                           <  3:235183/148‑1 (MQ=255)        aGCCCTTCGGCAATGAACAGAAACTCCACCCCGAACAGCCCGCCCGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGtgctgc                                                                                                                                          <  5:305451/149‑1 (MQ=255)          cccTTCGGCAATGAACAGAAACTCCACCCCGAACAGCCCGCCCGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCtt                                                                                                                                        <  3:291791/149‑1 (MQ=255)             ttCGGCAATGAACAGAAACTCCACCCCGAACAGCACGCCCGCCACCAGCCCTGTGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGc                                                                                                                                      >  7:277621/1‑148 (MQ=255)                 gCAATGAACAGAAACTCCACCCCGAACAGCCCGCCCGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCAc                                                                                                                                 >  3:304146/1‑149 (MQ=255)                      gAACAGAAACTCCACCCCGAACAGCCCGCCCGCCACCAGACCTGCGCGCCAGGTGCTGCCGACATGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGgcg                                                                                                                            >  6:3302/1‑149 (MQ=255)                        aCAGAAACTCCACCCCGAACAGCCCGCCCGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGTCATTG‑CGCAGTGCTGCTTGCATCACCGgcgc                                                                                                                           <  4:28595/148‑1 (MQ=255)                         cAGAAACTCCACCCCGAACAGCCCGCCCGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGa                                                                                                                         >  2:42854/1‑149 (MQ=255)                           gAAACTCCACCCCGAACAGCCCGCCCGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATg                                                                                                                       >  8:216844/1‑149 (MQ=255)                                  cACCCCGAACAGCCCGCCCGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGAcgg                                                                                                                >  3:301841/1‑149 (MQ=255)                                             gcccgcccGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCTGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTg                                                                                                     <  1:42854/149‑1 (MQ=255)                                             gcccgcccGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTg                                                                                                     <  4:304146/149‑1 (MQ=255)                                                cgcccgccACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATc                                                                                                  <  3:131056/149‑1 (MQ=255)                                                 gcccgccACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCa                                                                                                 <  7:216844/149‑1 (MQ=255)                                                 gcccgccACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCa                                                                                                 <  2:207662/149‑1 (MQ=255)                                                            gCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCa                                                                                                 <  4:70128/138‑1 (MQ=255)                                                            gCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCa                                                                                                 >  3:70128/1‑138 (MQ=255)                                                                  cgcgcCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTCCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGccc                                                                                >  8:285666/1‑149 (MQ=255)                                                                          gTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAg                                                                        <  3:56020/149‑1 (MQ=255)                                                                               gctgACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCa                                                                     >  8:43463/4‑147 (MQ=255)                                                                                 cGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAgg                                                                 >  6:325679/1‑149 (MQ=255)                                                                                    ccTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGcc                                                               >  1:293601/1‑148 (MQ=255)                                                                                     cTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCa                                                             <  1:288734/149‑1 (MQ=255)                                                                                                   cccGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTAcc                                                     >  4:166669/1‑143 (MQ=255)                                                                                                   cccGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTAcc                                                     <  3:166669/143‑1 (MQ=255)                                                                                                   cccGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAg                                               >  7:74038/1‑149 (MQ=255)                                                                                                    ccGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCt                                                    <  5:295351/143‑1 (MQ=255)                                                                                                    ccGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCt                                                    >  6:295351/1‑143 (MQ=255)                                                                                                     cGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAgg                                              >  7:10920/1‑148 (MQ=255)                                                                                                             cagcaTCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGt                                     >  4:297495/1‑149 (MQ=255)                                                                                                             cagcaTCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGt                                     <  5:325679/149‑1 (MQ=255)                                                                                                             cagcaTCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGt                                     <  5:3302/149‑1 (MQ=255)                                                                                                              agcaTCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CTCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGt                                                                                               <  5:201213/90‑1 (MQ=255)                                                                                                              agcaTCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTc                                    <  8:277621/149‑1 (MQ=255)                                                                                                              agcaTCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CACAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGt                                                                                               >  6:201213/1‑90 (MQ=255)                                                                                                                caTCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTg                                  >  6:294423/1‑149 (MQ=255)                                                                                                                  tCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTggg                                >  5:236964/1‑149 (MQ=255)                                                                                                                    aGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGt                               <  4:301841/148‑1 (MQ=255)                                                                                                                       ccTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCtt                           >  5:197852/1‑149 (MQ=255)                                                                                                                             aGCACTGC‑GCAATGGCATTGCCGCTGTGCTGCTTGCATCACCGGCGCGATGTCGACGTCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGAc                     >  2:158525/1‑149 (MQ=255)                                                                                                                             aGCACTGC‑GCAATGGCATTGCCGCTGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTgg                                                                                      <  3:285695/84‑1 (MQ=25)                                                                                                                             aGCACTGC‑GCAATGGCATTGCCGCTGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTgg                                                                                      >  4:285695/1‑84 (MQ=25)                                                                                                                              gCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGAcc                    >  7:253188/1‑149 (MQ=255)                                                                                                                              gCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGAcc                    <  7:285666/149‑1 (MQ=255)                                                                                                                              gCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGAcc                    <  3:297495/149‑1 (MQ=255)                                                                                                                               cacaGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGGAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGACcg                   <  8:253188/149‑1 (MQ=255)                                                                                                                               cacaGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGACcg                   <  8:10920/149‑1 (MQ=255)                                                                                                                                acaGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGACcgc                  >  5:125780/1‑149 (MQ=255)                                                                                                                                   gCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGACCgcgc                >  3:149325/1‑148 (MQ=255)                                                                                                                                            ccATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGACCGCGCTCATAAGCgg      >  3:285919/1‑149 (MQ=255)                                                                                                                                              aTTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGACCGCGCTCATAAGCGGGc    <  2:106560/149‑1 (MQ=255)                                                                                                                                                 g‑cgcAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGACCGCGCTCATAAGCGGGCct  <  4:285919/148‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                    CAGTTTCAGCCCTTCGGCAATGAACAGAAACTCCACCCCGAACAGCCCGCCCGCCACCAGCCCTGCGCGCCAGGTGCTGCCGACCTGCTCCCAGCCACCCCGCCAGCACAGCATCAGGCCTACCAGCACAGCGGCAATGCCATTG‑CGCAGTGCTGCTTGCATCACCGGCGCGATGTCGACGGCGGCGGTCTTGATCAGTACCTGCTGGCAGCCCCAGATCAGGCAAAGGCCCAGCATTACCTGGAAGGCAAAGGCGTCTGGGTTCTTGCGGACCGCGCTCATAAGCGGGCCT  >  NC_002947/5143502‑5143793

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: ‑