Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,081,877	T→C	intergenic (‑242/‑36)	tktA ← / → loiP	transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,081,877	0	T	C	100.0%	216.4 / NA	59	intergenic (‑242/‑36)	tktA/loiP	transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (32/27);  total (32/27)

TGGAACATCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTTTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGC  >  NC_000913/3081750‑3082007                                                                                                                                |                                                                                                                                   tGGAACATCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATc                                                                                                                         >  2:50680/1‑139 (MQ=255)      cATCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGAc                                                                                                                    >  1:1277401/1‑139 (MQ=255)       aTCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGAcc                                                                                                                   >  2:562526/1‑139 (MQ=255)       aTCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGAcc                                                                                                                   <  1:209342/139‑1 (MQ=255)       aTCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGAcc                                                                                                                   >  2:465059/1‑139 (MQ=255)         ccTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCtt                                                                                                                 >  1:413747/1‑139 (MQ=255)            tttGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTtgtg                                                                                                              <  1:562526/139‑1 (MQ=255)            tttGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTtgtg                                                                                                              <  2:415799/139‑1 (MQ=255)                   cTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAaga                                                                                                       >  1:25135/1‑139 (MQ=255)                                   aTCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTc                                                                                       >  2:137052/1‑139 (MQ=255)                                     cATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     <  2:1277401/139‑1 (MQ=255)                                     cATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     <  2:25135/139‑1 (MQ=255)                                      aTGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgcg                                                                                    >  2:72409/1‑139 (MQ=255)                                       tGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTtgtg                                                                                                              <  1:352196/112‑1 (MQ=255)                                       tGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTtgtg                                                                                                              >  2:352196/1‑112 (MQ=255)                                       tGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTc                                                                                       >  2:322235/1‑135 (MQ=255)                                       tGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTc                                                                                       <  1:322235/135‑1 (MQ=255)                                                                gCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCa                                                          <  1:245741/139‑1 (MQ=255)                                                                 cccGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCaa                                                         <  1:465059/139‑1 (MQ=255)                                                                 cccGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCaa                                                         <  2:413747/139‑1 (MQ=255)                                                                   cGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     >  1:699016/1‑109 (MQ=255)                                                                   cGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     <  2:699016/109‑1 (MQ=255)                                                                   cGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTAt                                                                              >  2:1238017/1‑116 (MQ=255)                                                                   cGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTAt                                                                              <  1:1238017/116‑1 (MQ=255)                                                                    gTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACgg                                                      >  1:225708/1‑139 (MQ=255)                                                                                  tCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGc                                        <  2:80218/139‑1 (MQ=255)                                                                                         actgagactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAata                                 <  1:87305/139‑1 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGaat                                                                                                                             >  1:689037/1‑43 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGaat                                                                                                                             <  2:689037/43‑1 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGaa                                                                                                                              >  1:736486/1‑42 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGaa                                                                                                                              <  2:736486/42‑1 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCg                                                                                                            >  1:663408/1‑60 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCg                                                                                                            <  2:663408/60‑1 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCgcgc                                                                                   >  1:768891/1‑85 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCgcgc                                                                                   <  2:768891/85‑1 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCgcgc                                                                                   <  2:223244/85‑1 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCgcgc                                                                                   >  1:223244/1‑85 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTATCAATGAGCGTGGCaa                                                         <  2:877777/111‑1 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCaa                                                         >  1:877777/1‑111 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGc                                        >  1:692819/1‑128 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGc                                        <  2:692819/128‑1 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             >  2:1180292/1‑139 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             >  2:958591/1‑139 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             >  1:24304/1‑139 (MQ=255)                                                                                             agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             >  2:157086/1‑139 (MQ=255)                                                                                              gactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGAc                            >  2:1002243/1‑139 (MQ=255)                                                                                                  gagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCa                        >  2:8851/1‑139 (MQ=255)                                                                                                   agCGTCGATTCACCTGCAAACGGCGCATTCTTAGaa                                                                                                                              >  2:612994/1‑36 (MQ=255)                                                                                                   agCGTCGATTCACCTGCAAACGGCGCATTCTTAGaa                                                                                                                              <  1:612994/36‑1 (MQ=255)                                                                                                   agCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     >  1:247962/1‑77 (MQ=255)                                                                                                   agCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     <  2:247962/77‑1 (MQ=255)                                                                                                   agCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGAGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCaa                       >  2:938060/1‑139 (MQ=255)                                                                                                     cGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACg                     <  1:157086/139‑1 (MQ=255)                                                                                                       tCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGa                   <  1:137052/139‑1 (MQ=255)                                                                                                                     aaCGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcg                                                                                      >  1:803333/1‑58 (MQ=255)                                                                                                                     aaCGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcg                                                                                      <  2:803333/58‑1 (MQ=255)                                                                                                                        ggCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGc  >  2:919601/1‑139 (MQ=255)                                                                                                                          cgcATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             >  1:146876/1‑110 (MQ=255)                                                                                                                          cgcATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             <  2:146876/110‑1 (MQ=255)                                                                                                                                |                                                                                                                                   TGGAACATCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTTTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGC  >  NC_000913/3081750‑3082007

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: ‑