Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,389,797	C→T	T93M (ACG→ATG)	aaeR →	transcriptional regulator for aaeXAB operon

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,389,797	0	C	T	100.0%	210.3 / NA	66	T93M (ACG→ATG)	aaeR	transcriptional regulator for aaeXAB operon
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (33/33);  total (33/33)

GTAGCACACGCAGCATTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGACGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGACCTGATTGCCGA  >  NC_000913/3389671‑3389929                                                                                                                               |                                                                                                                                     gTAGCACACGCAGCATTTGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTgg                                                                                                                          >  1:1364278/1‑139 (MQ=255)  tAGCACACGCAGCATTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGc                                                                                                                         >  1:914272/1‑139 (MQ=255)    gCACACGCAGCATTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTg                                                                                                                       <  2:1364278/139‑1 (MQ=255)          gcagcaTTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGttcttc                                                                                                                 <  1:628939/139‑1 (MQ=255)               aTTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTa                                                                                                            <  2:699761/139‑1 (MQ=255)                        aCCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGttcttc                                                                                                                 <  2:1361685/125‑1 (MQ=255)                        aCCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGttcttc                                                                                                                 >  1:1361685/1‑125 (MQ=255)                        aCCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACaaa                                                                                                   >  1:148791/1‑139 (MQ=255)                                                cAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCa                                                                           <  1:817568/139‑1 (MQ=255)                                                       gCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGc                                                                                                                         <  2:1182631/86‑1 (MQ=255)                                                       gCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGc                                                                                                                         >  1:1182631/1‑86 (MQ=255)                                                             gtATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGa                                                              <  2:393643/139‑1 (MQ=255)                                                              tATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCt                                                                                                                        >  2:365335/1‑80 (MQ=255)                                                              tATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCt                                                                                                                        <  1:365335/80‑1 (MQ=255)                                                                  cTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCt                                                                                                                        <  2:359305/76‑1 (MQ=255)                                                                  cTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCt                                                                                                                        >  1:359305/1‑76 (MQ=255)                                                                   ttCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATAccc                                                        <  2:148791/139‑1 (MQ=255)                                                                     cATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAg                                                      >  1:931002/1‑139 (MQ=255)                                                                         aaGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGttt                                                  <  2:914272/139‑1 (MQ=255)                                                                            tGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTtctc                                                                                           >  1:312103/1‑95 (MQ=255)                                                                            tGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTtctc                                                                                           <  2:312103/95‑1 (MQ=255)                                                                                  aTGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCaa                                         <  2:931002/139‑1 (MQ=255)                                                                                   tGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCAGAAAATGTtct                                                                                            >  2:1024217/1‑87 (MQ=255)                                                                                   tGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTtct                                                                                            <  1:1024217/87‑1 (MQ=255)                                                                                      tCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATAcc                                                         >  2:963891/1‑119 (MQ=255)                                                                                      tCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATAcc                                                         <  1:963891/119‑1 (MQ=255)                                                                                      tCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTg                                     >  1:701708/1‑139 (MQ=255)                                                                                           aGCAACTGTATGCCTTCAATAACACCCACATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGACAATCTGGTTAc                                >  2:852180/1‑139 (MQ=255)                                                                                             cAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCg                                             <  1:1071165/124‑1 (MQ=255)                                                                                             cAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCg                                             >  2:1071165/1‑124 (MQ=255)                                                                                               aCTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGc                                                                                                        <  2:1191327/63‑1 (MQ=255)                                                                                               aCTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGc                                                                                                        >  1:1191327/1‑63 (MQ=255)                                                                                               aCTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACaaa                                                                                                   >  2:1125270/1‑68 (MQ=255)                                                                                               aCTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACaaa                                                                                                   <  1:1125270/68‑1 (MQ=255)                                                                                               aCTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGTCGGGCTGACAGCCAAAATGCTGa                                                                  <  1:921874/101‑1 (MQ=255)                                                                                               aCTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGTCGGGCTGACAGCCAAAATGCTGa                                                                  >  2:921874/1‑101 (MQ=255)                                                                                                  gTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAAtt                         >  1:432131/1‑139 (MQ=255)                                                                                                    aTGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTcc                       >  1:543291/1‑139 (MQ=255)                                                                                                     tGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCa                      <  2:701708/139‑1 (MQ=255)                                                                                                          tCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGa                                                              <  1:292451/94‑1 (MQ=255)                                                                                                          tCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGa                                                              >  2:292451/1‑94 (MQ=255)                                                                                                          tCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAAt                                        <  1:93754/116‑1 (MQ=255)                                                                                                          tCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAAt                                        >  2:93754/1‑116 (MQ=255)                                                                                                           cAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGccccc                >  1:1250279/1‑139 (MQ=255)                                                                                                             aTAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGa              >  2:246788/1‑139 (MQ=255)                                                                                                                 cacCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAAt                                        <  1:67182/109‑1 (MQ=255)                                                                                                                 cacCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAAt                                        >  2:67182/1‑109 (MQ=255)                                                                                                                 cacCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGACCTg          >  1:18076/1‑139 (MQ=255)                                                                                                                  acCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATAc                                                          >  1:643601/1‑90 (MQ=255)                                                                                                                  acCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATAc                                                          <  2:643601/90‑1 (MQ=255)                                                                                                                   cccccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGa                                                              <  1:371100/85‑1 (MQ=255)                                                                                                                   cccccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGa                                                              >  2:371100/1‑85 (MQ=255)                                                                                                                     cccATCGGGATGCTACGCATTGGCTGTTCTTCAACTAt                                                                                                           <  2:161601/38‑1 (MQ=38)                                                                                                                     cccATCGGGATGCTACGCATTGGCTGTTCTTCAACTAt                                                                                                           >  1:161601/1‑38 (MQ=255)                                                                                                                      ccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCt                                                                                   <  2:95651/61‑1 (MQ=255)                                                                                                                      ccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCt                                                                                   >  1:95651/1‑61 (MQ=255)                                                                                                                      ccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCaaaa                                                                        >  2:508139/1‑72 (MQ=255)                                                                                                                      ccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCaaaa                                                                        <  1:508139/72‑1 (MQ=255)                                                                                                                      ccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAAt                                        >  2:724496/1‑104 (MQ=255)                                                                                                                      ccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAAt                                        <  1:724496/104‑1 (MQ=255)                                                                                                                      ccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGACCTGATTGc     >  2:1149448/1‑139 (MQ=255)                                                                                                                        aTCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAg                                               <  1:130523/95‑1 (MQ=255)                                                                                                                        aTCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAg                                               >  2:130523/1‑95 (MQ=255)                                                                                                                         tCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGACCTGATTGCCGa  <  2:1250279/139‑1 (MQ=255)                                                                                                                         tCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAAGGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGACCTGATTGCCGa  <  2:1120272/139‑1 (MQ=255)                                                                                                                         tCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCAGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGTCCTGATTGCCGa  <  1:392580/139‑1 (MQ=255)                                                                                                                               |                                                                                                                                     GTAGCACACGCAGCATTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGACGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGACCTGATTGCCGA  >  NC_000913/3389671‑3389929

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑