Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,664,986	C→T	*275* (TAG→TAA)	gadX ←	acid resistance regulon transcriptional activator, autoactivator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,664,986	0	C	T	100.0%	195.1 / NA	61	*275* (TAG→TAA)	gadX	acid resistance regulon transcriptional activator, autoactivator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (31/30);  total (31/30)

TTATATTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTCTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCAT  >  NC_000913/3664851‑3665111                                                                                                                                          |                                                                                                                              ttATATTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTtat                                                                                                                            <  1:1313986/139‑1 (MQ=255)    tatTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAAt                                                                                                                         <  1:552366/139‑1 (MQ=255)         aaCTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAAt                                                                                                                         >  2:1440242/1‑134 (MQ=255)         aaCTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAAt                                                                                                                         <  1:1440242/134‑1 (MQ=255)                      cacaAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGaa                                                                                                       >  1:1089540/1‑139 (MQ=255)                        caAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACg                                                                                                     >  2:561629/1‑139 (MQ=255)                             tttCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAg                                                                                                <  2:1604943/139‑1 (MQ=255)                                     gCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAg                                                                                                <  2:1356207/131‑1 (MQ=255)                                     gCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAg                                                                                                >  1:1356207/1‑131 (MQ=255)                                       cAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGt                                                                                                   >  2:389836/1‑126 (MQ=255)                                       cAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGt                                                                                                   <  1:389836/126‑1 (MQ=255)                                       cAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGc                                                                                             >  1:635936/1‑132 (MQ=255)                                       cAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGc                                                                                             <  2:635936/132‑1 (MQ=255)                                             ggAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                        >  2:1356837/1‑115 (MQ=255)                                             ggAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                        <  1:1356837/115‑1 (MQ=255)                                              gAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGGTTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTccc                                                                                >  2:1497455/1‑139 (MQ=255)                                               aGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                        <  1:1028231/113‑1 (MQ=255)                                               aGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                        >  2:1028231/1‑113 (MQ=255)                                               aGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCtt                                                                              >  1:1157629/1‑139 (MQ=255)                                                           gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgcg                                                                           <  2:459178/130‑1 (MQ=255)                                                           gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgcg                                                                           >  1:459178/1‑130 (MQ=255)                                                             ttattaGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACtt                                                                >  1:447615/1‑139 (MQ=255)                                                             ttattaGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACtt                                                                >  2:494117/1‑139 (MQ=255)                                                             ttattaGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACtt                                                                >  1:924407/1‑139 (MQ=255)                                                              tattaGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTccc                                                                                <  1:407177/122‑1 (MQ=255)                                                              tattaGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTccc                                                                                >  2:407177/1‑122 (MQ=255)                                                                        gagaCGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgcg                                                                           <  2:1200403/117‑1 (MQ=255)                                                                        gagaCGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgcg                                                                           >  1:1200403/1‑117 (MQ=255)                                                                             ggCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGt                                                >  2:791219/1‑139 (MQ=255)                                                                              gCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGtt                                               >  2:1383438/1‑139 (MQ=255)                                                                              gCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGtt                                               >  1:511152/1‑139 (MQ=255)                                                                               cAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTc                                              <  2:1157629/139‑1 (MQ=255)                                                                                  accaaccTCTTTCCCGTCCCCTTATGCCGGG‑TTTTTTTATTGCCTAAGTAAACCTTTATAA‑CCTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                           <  2:533513/134‑1 (MQ=255)                                                                                  aCTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                           <  1:1260960/139‑1 (MQ=255)                                                                                  aCTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                           <  2:547584/139‑1 (MQ=255)                                                                                            tCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttcc                                                                                                                 >  2:428315/1‑59 (MQ=255)                                                                                            tCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttcc                                                                                                                 <  1:428315/59‑1 (MQ=255)                                                                                             cccGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATC‑TACTTCTTCCGGAGAACCGGCAGGGCCGGAAAAATTTCCTTCCGCAACAAATATTGCCGCCGAGGCACGGTTCGATAATCTCTCCGcc                               >  1:533513/1‑139 (MQ=255)                                                                                                ggTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgc                                                                            >  2:1491205/1‑92 (MQ=255)                                                                                                ggTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgc                                                                            <  1:1491205/92‑1 (MQ=255)                                                                                                 gTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGAt                            <  2:924407/139‑1 (MQ=255)                                                                                                  tCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCg                              <  2:146341/136‑1 (MQ=255)                                                                                                  tCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCg                              >  1:146341/1‑136 (MQ=255)                                                                                                   cccc‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAATCACGGTTCGACAATCTCTGCGCCGATCg                          >  1:675995/1‑139 (MQ=255)                                                                                                    ccc‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                         <  2:511152/139‑1 (MQ=255)                                                                                                     cc‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTTCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGa                             <  1:1239838/134‑1 (MQ=255)                                                                                                     cc‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTTCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGa                             >  2:1239838/1‑134 (MQ=255)                                                                                                     cc‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                         <  1:631826/138‑1 (MQ=255)                                                                                                     cc‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                         >  2:631826/1‑138 (MQ=255)                                                                                                      c‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTc                       <  2:1089540/139‑1 (MQ=255)                                                                                                        tATGCCGTG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTg                                                                             <  1:1195713/84‑1 (MQ=255)                                                                                                        tATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTg                                                                             >  2:1195713/1‑84 (MQ=255)                                                                                                               gg‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATAct               >  2:316426/1‑139 (MQ=255)                                                                                                                   tttttttATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCtg            <  2:195803/139‑1 (MQ=255)                                                                                                                            gTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGt     >  1:989483/1‑137 (MQ=255)                                                                                                                            gTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGt     <  2:989483/137‑1 (MQ=255)                                                                                                                            gTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCa   <  1:1383438/139‑1 (MQ=255)                                                                                                                                 aGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGt     <  2:1327768/132‑1 (MQ=255)                                                                                                                                 aGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGt     >  1:1327768/1‑132 (MQ=255)                                                                                                                                      aaCTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCAt  >  2:218353/1‑130 (MQ=255)                                                                                                                                      aaCTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCAt  <  1:218353/130‑1 (MQ=255)                                                                                                                                          |                                                                                                                              TTATATTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑TATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTCTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCAT  >  NC_000913/3664851‑3665111

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑