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%	143.3 / NA	46	T93M (ACG→ATG)	aaeR	transcriptional regulator for aaeXAB operon
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (24/22);  total (24/22)

TAAACCGTAGCACACGCAGCATTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGACGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGACCTGATTGCCGA  >  NC_000913/3389665‑3389929                                                                                                                                     |                                                                                                                                     tAAACCGTAGCACACGCAGCATTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACg                                                                                                                                >  1:1176867/1‑139 (MQ=255)        tAGCACACGCAGCATTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGc                                                                                                                         >  1:1214008/1‑139 (MQ=255)        tAGCACACGCAGCATTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGc                                                                                                                         <  2:123752/139‑1 (MQ=255)           cacaCGCAGCATTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGt                                                                                                                      <  2:1214008/139‑1 (MQ=255)             cacGCAGCATTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGttc                                                                                                                    >  1:154359/1‑139 (MQ=255)                   gcaTTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAAc                                                                                                              <  2:154359/139‑1 (MQ=255)                    caTTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACt                                                                                                             >  1:535513/1‑139 (MQ=255)                      ttGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTAt                                                                                                           <  2:1176867/139‑1 (MQ=255)                      ttGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTAt                                                                                                           <  1:846241/139‑1 (MQ=255)                              aCCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCt                                                                                                                        >  1:1145225/1‑118 (MQ=255)                              aCCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCt                                                                                                                        <  2:1145225/118‑1 (MQ=255)                                                        gggCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCaaa                                                                         >  1:702305/1‑139 (MQ=255)                                                                        cTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTg                                                                                                                       <  2:175033/77‑1 (MQ=255)                                                                        cTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTg                                                                                                                       >  1:175033/1‑77 (MQ=255)                                                                              gAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGtt                                                   >  2:988903/1‑139 (MQ=255)                                                                                       gATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCa                                          >  2:175089/1‑139 (MQ=255)                                                                                            tCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGc                                                                                                                         >  1:474916/1‑55 (MQ=255)                                                                                            tCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGc                                                                                                                         <  2:474916/55‑1 (MQ=255)                                                                                            tCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCt                                                                                                                        <  1:759498/56‑1 (MQ=255)                                                                                            tCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCt                                                                                                                        >  2:759498/1‑56 (MQ=255)                                                                                            tCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTg                                                                   >  1:368800/1‑109 (MQ=255)                                                                                            tCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTg                                                                   <  2:368800/109‑1 (MQ=255)                                                                                                          aTGCCTTCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTcc                       <  2:702305/139‑1 (MQ=255)                                                                                                                tCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGttt                                                  <  2:1213402/106‑1 (MQ=255)                                                                                                                tCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGttt                                                  >  1:1213402/1‑106 (MQ=255)                                                                                                                tCAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGcccc                 >  2:73018/1‑139 (MQ=255)                                                                                                                 cAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGca                                                                                                       <  1:915325/52‑1 (MQ=255)                                                                                                                 cAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGca                                                                                                       >  2:915325/1‑52 (MQ=255)                                                                                                                 cAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGca                                                                                                       >  2:325755/1‑52 (MQ=255)                                                                                                                 cAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGca                                                                                                       <  1:325755/52‑1 (MQ=255)                                                                                                                 cAATAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGccccc                >  1:5689/1‑139 (MQ=255)                                                                                                                    tAACACCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGAc             <  1:988903/139‑1 (MQ=255)                                                                                                                       cacCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGa                                                              >  1:518461/1‑87 (MQ=255)                                                                                                                       cacCCCCATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGa                                                              <  2:518461/87‑1 (MQ=255)                                                                                                                          ccccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGACCTGAtt       >  2:981701/1‑139 (MQ=255)                                                                                                                            ccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGAc                                                                                <  2:82061/64‑1 (MQ=255)                                                                                                                            ccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGAc                                                                                >  2:1130411/1‑64 (MQ=255)                                                                                                                            ccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGAc                                                                                <  1:1130411/64‑1 (MQ=255)                                                                                                                            ccATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGAc                                                                                >  1:82061/1‑64 (MQ=255)                                                                                                                             cATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAAt                                        <  1:88029/103‑1 (MQ=255)                                                                                                                             cATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAAt                                        >  2:88029/1‑103 (MQ=255)                                                                                                                             cATCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGACCTGATTGcc    <  1:438043/139‑1 (MQ=255)                                                                                                                              aTCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATg                                                                                                <  2:773923/46‑1 (MQ=255)                                                                                                                              aTCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATg                                                                                                >  1:773923/1‑46 (MQ=255)                                                                                                                               tCGGGATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGACCTGATTGCCGa  <  1:73018/139‑1 (MQ=255)                                                                                                                                  ggATGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCaaaa                                                                        >  2:993363/1‑66 (MQ=255)                                                                                                                                     |                                                                                                                                     TAAACCGTAGCACACGCAGCATTGGCCTGACCGAAGCCGGTAGAATTTACTACCAGGGCTGCCGTCGTATGCTTCATGAAGTGCAGGATGTTCATGAGCAACTGTATGCCTTCAATAACACCCCCATCGGGACGCTACGCATTGGCTGTTCTTCAACTATGGCACAAAATGTTCTCGCCGGGCTGACAGCCAAAATGCTGAAAGAATACCCAGGTTTGAGCGTCAATCTGGTTACCGGAATTCCAGCCCCCGACCTGATTGCCGA  >  NC_000913/3389665‑3389929

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: ‑