Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,100,288	C→A	G80C (GGC→TGC)	rhaT ←	rhamnose/lyxose:H(+) symporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,100,288	0	C	A	100.0%	190.8 / NA	55	G80C (GGC→TGC)	rhaT	rhamnose/lyxose:H(+) symporter
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (28/27);  total (28/27)

CCGTTGATAATTGGCGTCATCAGCGTACCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCCGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACCACATGGTTTCC  >  NC_000913/4100158‑4100424                                                                                                                                   |                                                                                                                                         ccGTTGATAATTGGCGTCATCAGCGTACCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGaaa                                                                                                                                 >  1:851979/1‑140 (MQ=255) ccGTTGATAATTGGCGTCATCAGCGTACCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATAGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGaca                                                                                                                                 >  2:109282/1‑138 (MQ=255)         aaTTGGCGTCATCAGCGTACCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCa                                                                                                                         <  2:850058/140‑1 (MQ=255)                gTCATCAGCGTACCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGt                                                                                                                  >  2:90462/1‑140 (MQ=255)                gTCATCAGCGTACCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGT‑‑‑‑CCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTagag                                                                                                              >  1:591150/1‑140 (MQ=255)                 tcatcaGCGTACCGACAATCAACGTAATGCTAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTa                                                                                                                 >  1:787313/1‑140 (MQ=255)                  catcaGCGTACCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTag                                                                                                                <  1:387157/140‑1 (MQ=255)                  catcaGCGTACCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTag                                                                                                                <  1:71173/140‑1 (MQ=255)                   atcaGCGTACCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTaga                                                                                                               >  2:42600/1‑140 (MQ=255)                   atcaGCGTACCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTaga                                                                                                               <  1:125934/140‑1 (MQ=255)                           aCCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTaa                                                                                                       <  1:90462/140‑1 (MQ=255)                             cGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAAc                                                                                                     <  1:246723/140‑1 (MQ=255)                                cAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAg                                                                                                  <  1:808272/140‑1 (MQ=255)                                cAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGAAAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAg                                                                                                  <  2:716/140‑1 (MQ=255)                                  aTCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCt                                                                                                >  2:123570/1‑140 (MQ=255)                                           aTGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGc                                                                                       >  2:638176/1‑140 (MQ=255)                                                   ggCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCTCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAAt                                                                               <  2:519623/140‑1 (MQ=255)                                                       aTGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCgg                                                                           >  1:1052200/1‑140 (MQ=255)                                                                        cATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGa                                                          <  2:851979/140‑1 (MQ=255)                                                                          tGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATg                                                        >  1:43076/1‑140 (MQ=255)                                                                           gCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATgg                                                       >  2:95891/1‑140 (MQ=255)                                                                           gCCGAGATAACGCATGGT‑‑‑‑CCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCa                                                   <  2:591150/140‑1 (MQ=255)                                                                             cGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGcc                                                     <  1:499099/140‑1 (MQ=255)                                                                             cGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGcc                                                     <  1:123570/140‑1 (MQ=255)                                                                                  tAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACgg                                                <  2:787313/140‑1 (MQ=255)                                                                                     cGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCa                                                   <  1:650368/134‑1 (MQ=255)                                                                                     cGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCa                                                   >  2:650368/1‑134 (MQ=255)                                                                                         tGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGaata                                         <  1:42600/140‑1 (MQ=255)                                                                                          ggTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGaataa                                        >  1:457715/1‑140 (MQ=255)                                                                                          ggTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGaataa                                        >  1:306049/1‑140 (MQ=255)                                                                                               ggCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCa                                    <  1:785918/139‑1 (MQ=255)                                                                                               ggCCGTAGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCa                                    >  2:785918/1‑139 (MQ=255)                                                                                                     aGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCATTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACa                             >  1:186606/1‑140 (MQ=255)                                                                                                     aGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACa                             >  1:1015092/1‑140 (MQ=255)                                                                                                     aGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACa                             >  2:956382/1‑140 (MQ=255)                                                                                                     aGTTGATATTACCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACa                             <  2:43076/140‑1 (MQ=255)                                                                                                               aCCGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGa                   >  1:474897/1‑140 (MQ=255)                                                                                                                 cGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACt                 <  1:638176/140‑1 (MQ=255)                                                                                                                 cGATCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACt                 <  1:956382/140‑1 (MQ=255)                                                                                                                    tCCCCCACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGAc              >  2:916163/1‑140 (MQ=255)                                                                                                                     cccccACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGAcc             <  2:329140/140‑1 (MQ=255)                                                                                                                     cccccACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGAcc             >  2:467806/1‑140 (MQ=255)                                                                                                                       cccACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACcac           <  2:457715/140‑1 (MQ=255)                                                                                                                       cccACATAGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACcac           <  2:124952/140‑1 (MQ=255)                                                                                                                       cccACATAGCGCAGAACAGAAAAACAGGAAGTCGCGTAGAGAGACTAAACGAGCTGTAGTACGCCCAGAACTTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGTAACAAGCCCACCGACTGAcctc           <  2:422534/140‑3 (MQ=255)                                                                                                                              aGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACcac           <  2:297323/133‑1 (MQ=255)                                                                                                                              aGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACcac           >  1:297323/1‑133 (MQ=255)                                                                                                                              aGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACCACATGGttt    >  1:941685/1‑140 (MQ=255)                                                                                                                              aGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACCACATGGttt    >  1:42254/1‑140 (MQ=255)                                                                                                                              aGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACCACATGGttt    >  1:467993/1‑140 (MQ=255)                                                                                                                              aGCGCAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAAACCCACCGACTGACCACATGGttt    >  1:151389/1‑140 (MQ=255)                                                                                                                               gcgcAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACCACATgg       >  2:223438/1‑136 (MQ=255)                                                                                                                               gcgcAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACCACATgg       <  1:223438/136‑1 (MQ=255)                                                                                                                               gcgcAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACCACATGGTTTc   >  2:455324/1‑140 (MQ=255)                                                                                                                                cgcAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAATCAATCCCACCGACTGACCACATGGTTTcc  >  1:390128/1‑140 (MQ=255)                                                                                                                                cgcAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACt                 <  2:1032144/125‑1 (MQ=255)                                                                                                                                cgcAGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACcac           <  1:674545/131‑1 (MQ=255)                                                                                                                                   |                                                                                                                                         CCGTTGATAATTGGCGTCATCAGCGTACCGACAATCAACGTAATGCCAATGGCGATGCCAATTCCCATCGACATGCCGAGATAACGCATGGTCAGGCCGTAGTTGATATTACCGATCCCCCACATAGCGCCGAACAGAAAAACAGGCAGTCGCGTAGAGAGACTAAACGAGCTGTAATACGCCCAGAAATTCGGTAGTAACAGGGCGCTGATGGCCCACGGCAGAATAATCCACGAAACAATCCCACCGACTGACCACATGGTTTCC  >  NC_000913/4100158‑4100424

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑