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%	177.2 / NA	55	*275* (TAG→TAA)	gadX	acid resistance regulon transcriptional activator, autoactivator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (28/27);  total (28/27)

TTATATTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTCTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCA  >  NC_000913/3664851‑3665115                                                                                                                                         |                                                                                                                                  ttATATTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTGTGTCTGAGTAAAACTTtat                                                                                                                                <  2:984494/139‑1 (MQ=255)           cTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAt                                                                                                                        <  2:642213/137‑1 (MQ=255)           cTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAt                                                                                                                        >  1:642213/1‑137 (MQ=255)                    agCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTta                                                                                                                                 >  2:615785/1‑119 (MQ=255)                    agCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTta                                                                                                                                 <  1:615785/119‑1 (MQ=255)                      cacaAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGaa                                                                                                           >  1:1121041/1‑139 (MQ=255)                      cacaAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGaa                                                                                                           >  1:1155230/1‑139 (MQ=255)                      cacaAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGaa                                                                                                           >  1:1251114/1‑139 (MQ=255)                      cacaAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                            <  1:1164422/138‑1 (MQ=255)                      cacaAAGTTTCCCGTGCCAACAGGGAGTATTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                            >  2:1164422/1‑138 (MQ=255)                          aaGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGt                                                                                                       <  2:1121041/139‑1 (MQ=255)                                cccGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttcc                                                                                                                     >  2:275970/1‑120 (MQ=255)                                cccGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGGTTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttcc                                                                                                                     <  1:275970/120‑1 (MQ=255)                                     gCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTaa                                                                                            >  2:1610003/1‑139 (MQ=255)                                              gAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCt                                                                                   >  1:940941/1‑139 (MQ=255)                                               aGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGt                                                                                                       <  2:754866/118‑1 (MQ=255)                                               aGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGt                                                                                                       >  1:754866/1‑118 (MQ=255)                                               aGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCtt                                                                                  >  2:1746849/1‑139 (MQ=255)                                                gtgtTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTg                                                                                 >  1:456072/1‑139 (MQ=255)                                                           gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGt                                                                                                       <  1:1066984/106‑1 (MQ=255)                                                           gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGt                                                                                                       >  2:1066984/1‑106 (MQ=255)                                                           gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAg                                                                                                    >  1:312769/1‑109 (MQ=255)                                                           gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAg                                                                                                    <  2:312769/109‑1 (MQ=255)                                                           gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATAc                                                                      >  1:463027/1‑139 (MQ=255)                                                                   gTCTGGAGACGGCAGACGATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTgccgct                                                              <  2:1155230/139‑2 (MQ=255)                                                                       ggAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGt                                                          <  2:463027/139‑1 (MQ=255)                                                                         agaCGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCa                                                        <  1:1269215/139‑1 (MQ=255)                                                                         agaCGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCa                                                        <  1:1746849/139‑1 (MQ=255)                                                                              gCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTta                                                                                                                                 <  1:895195/61‑1 (MQ=255)                                                                              gCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTta                                                                                                                                 >  2:895195/1‑61 (MQ=255)                                                                                  aCTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGt                                                          >  1:202588/1‑128 (MQ=255)                                                                                  aCTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGt                                                          <  2:202588/128‑1 (MQ=255)                                                                                  aCTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                               <  2:1251114/139‑1 (MQ=255)                                                                                  aCTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                               >  1:1665961/1‑139 (MQ=255)                                                                                                ggTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAg                                                                                                    <  2:619604/72‑1 (MQ=255)                                                                                                ggTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAg                                                                                                    <  2:371693/72‑1 (MQ=255)                                                                                                ggTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAg                                                                                                    >  1:371693/1‑72 (MQ=255)                                                                                                ggTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAg                                                                                                    >  1:619604/1‑72 (MQ=255)                                                                                                  tCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATc                               >  1:533310/1‑139 (MQ=255)                                                                                                    cccTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                             <  2:533310/139‑1 (MQ=255)                                                                                                              gg‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCtt                                                                                                                          <  2:886256/36‑1 (MQ=255)                                                                                                              gg‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCtt                                                                                                                          >  1:886256/1‑36 (MQ=255)                                                                                                              gg‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGa                                 >  1:282805/1‑125 (MQ=255)                                                                                                              gg‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGa                                 <  2:282805/125‑1 (MQ=255)                                                                                                              gg‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATAct                   <  2:940941/139‑1 (MQ=255)                                                                                                              gg‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATAct                   >  1:820210/1‑139 (MQ=255)                                                                                                                 ttttttttATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGcc                                                                                                >  1:1566860/1‑60 (MQ=255)                                                                                                                 ttttttttATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGcc                                                                                                <  2:1566860/60‑1 (MQ=255)                                                                                                                       ttATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGc           <  2:820210/139‑1 (MQ=255)                                                                                                                         aTGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCa                                                        <  1:258573/92‑1 (MQ=255)                                                                                                                         aTGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCa                                                        >  2:258573/1‑92 (MQ=255)                                                                                                                           gTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCa       <  2:1665961/139‑1 (MQ=255)                                                                                                                               gAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGt         >  2:1780163/1‑133 (MQ=255)                                                                                                                               gAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGt         <  1:1780163/133‑1 (MQ=255)                                                                                                                                aGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCa  >  1:1027478/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                  TTATATTTAACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTCTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCA  >  NC_000913/3664851‑3665115

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑