Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,849,315	A→C	Y540S (TAC→TCC)	flhA →	formate hydrogenlyase transcriptional activator FlhA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,849,315	0	A	C	100.0%	237.9 / NA	64	Y540S (TAC→TCC)	flhA	formate hydrogenlyase transcriptional activator FlhA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (32/32);  total (32/32)

TCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTT  >  NZ_CP009273/2849229‑2849399                                                                                       |                                                                                     tCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCg                                                                                   >  2:58723/1‑90 (MQ=255)    gacggacgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCt                                                                                >  1:546436/1‑90 (MQ=255)      cggacgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGa                                                                              >  1:218959/1‑90 (MQ=255)       ggacgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGaa                                                                             >  1:906798/1‑90 (MQ=255)        gacgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAAc                                                                            >  2:1296181/1‑90 (MQ=255)         acgTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACg                                                                           >  2:706710/1‑90 (MQ=255)                 cTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCg                                                                   <  2:2465346/90‑1 (MQ=255)                  tAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGaa                                                                             <  1:2565548/79‑1 (MQ=255)                  tAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGaa                                                                             >  2:2565548/1‑79 (MQ=255)                   aaTCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGAt                                                                 >  1:2829904/1‑90 (MQ=255)                     tCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTc                                                               <  1:273099/90‑1 (MQ=255)                       gccgcGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCAc                                                             >  1:1644622/1‑90 (MQ=255)                       gccgcGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCAc                                                             <  2:2223983/90‑1 (MQ=255)                       gccgcGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCAc                                                             >  1:2475908/1‑90 (MQ=255)                        ccgcGACTACCCGCGATCTAAAAAAATGGGTCGCCGCCCGTGAGTCCCGTAGCGATCTTTTTTCCCGCCTGAACGTATTCCCGATTcccc                                                            <  1:1396455/90‑1 (MQ=255)                        ccgcGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCAcc                                                            >  2:1396455/1‑90 (MQ=255)                        ccgcGACTAACCGCGATCTGAAAAAAATGGTCCCCGCCCGTGGGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTcccc                                                            >  1:2003665/1‑90 (MQ=255)                           cgACTACCCGCGATCTAAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCCCCTgc                                                         <  1:513172/90‑1 (MQ=255)                           cgACAACCCGCGATCTAAAAAAAATGGTCCCCGCCCGTGATTCCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCCCCTgc                                                         <  1:849734/90‑1 (MQ=255)                            gACTACCCGCGATCTAAAAAAAAGGGTCGCCGCCCGTGAGTCCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgcc                                                        <  1:659311/90‑1 (MQ=255)                               tacccGCGTTTTGAAAAAATGGGTCCCCGCCCGGGAGTCCCGTAGGGATCTCTTTTCCCGCCTGAACGTATTCCCGATTCACCTgccgcc                                                     <  1:2813324/87‑1 (MQ=255)                               tAACCGCGATCTGAAAAAAATGGTCGCCGCCCGTGATTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgccgcc                                                     <  1:2365822/90‑1 (MQ=255)                               tAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgccgcc                                                     <  2:546436/90‑1 (MQ=255)                                  ccGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACt                                                  >  1:120717/1‑90 (MQ=255)                                      gATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTAcgc                                              >  1:382672/1‑90 (MQ=255)                                        tCTAAAAAAATCGGCCGCCGCCGGTGATTCCCGAAGCGATCTCTATCCCCGCCTGAACTTTTCCCCGATTACCCTGCCGCCACTACGCGa                                            <  1:2391955/90‑1 (MQ=255)                                         gtaaaaaaaaTGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATCCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAg                                           <  2:2125200/87‑1 (MQ=255)                                         ctaaaaaaaaTGGTCGCCGCCCGTGAGTCCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAg                                           <  1:1077425/87‑1 (MQ=255)                                         cTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAg                                           <  2:169630/90‑1 (MQ=255)                                         cTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAg                                           <  2:646494/90‑1 (MQ=255)                                          tGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGc                                          <  2:906798/90‑1 (MQ=255)                                           gAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCg                                         >  1:1479129/1‑90 (MQ=255)                                           gAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCg                                         <  2:766615/90‑1 (MQ=255)                                           aaaaaaaaTGGTCGCCGTCCGTGACTTCCGTAGCGACCTTTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCg                                         <  2:2249276/89‑1 (MQ=255)                                               aaaaTGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCCCTACGCGAGCGTCCg                                     <  1:763396/90‑1 (MQ=255)                                                aaaGGGTCGCCGCCCGTGAGTTCCGTGGCGTTCTCTTTCCCCGCCTGAACGTTTTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCgg                                    <  1:2233112/90‑1 (MQ=255)                                                  aTGGTCGCCACCCGGGAATCCCGAAGCGATCTTTATTCCCGCCTGAACGTATTCCCGATCCACCTGCCGCCACTACGCGAGCGTCCGGaa                                  <  2:1303884/90‑1 (MQ=255)                                                     gTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGat                               >  1:610176/1‑90 (MQ=255)                                                          cGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTcc                          >  2:1732907/1‑90 (MQ=255)                                                           gACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCg                         >  2:2753951/1‑90 (MQ=255)                                                            aCCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCgc                        <  1:207070/90‑1 (MQ=255)                                                               gTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCgctgc                     >  1:1431008/1‑90 (MQ=255)                                                                     tCCGTGGCGATCTCTTTCCCCCCCTGAACGTTTTCCCGATCCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGa               <  1:906257/90‑1 (MQ=37)                                                                     tCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGa               >  2:668662/1‑90 (MQ=255)                                                                     cccGTAGCGATCTCTATCCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGa               <  1:807685/89‑1 (MQ=39)                                                                      ccGTAGCGCTCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaa              <  2:2647519/90‑1 (MQ=255)                                                                      ccGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaa              <  2:1388530/90‑1 (MQ=255)                                                                      ccGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaa              <  2:1851529/90‑1 (MQ=255)                                                                        gTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgccgcc                                                     >  2:2102804/1‑49 (MQ=255)                                                                        gTAGCGATCTCTATCCCCGCCTGAACGTATTCCCGATTCACCTgccgcc                                                     <  1:2102804/49‑1 (MQ=38)                                                                             gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGa               >  1:2384494/1‑82 (MQ=255)                                                                             gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGa               <  2:2384494/82‑1 (MQ=255)                                                                             gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCttt       >  2:2001823/1‑90 (MQ=255)                                                                             gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCttt       >  2:1802504/1‑90 (MQ=255)                                                                             gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCttt       >  1:1832414/1‑90 (MQ=255)                                                                             gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCttt       >  2:720762/1‑90 (MQ=255)                                                                             gATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCttt       >  1:1085738/1‑90 (MQ=255)                                                                              aTCTCTTTTCCCGCCTGAACGTATTCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTa      <  2:1563378/90‑1 (MQ=39)                                                                              aTCTCTTTCCCCGCCTGAACGTTTTCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTa      <  1:706710/90‑1 (MQ=38)                                                                                ctctATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTAcc    >  1:2996918/1‑90 (MQ=255)                                                                                ctctATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTAcc    >  2:194100/1‑90 (MQ=255)                                                                                ctctATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTAcc    >  1:3018703/1‑90 (MQ=255)                                                                                ctctATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTAcc    >  2:1435592/1‑90 (MQ=255)                                                                                  ctATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCtt  >  1:359553/1‑90 (MQ=255)                                                                                       |                                                                                     TCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTT  >  NZ_CP009273/2849229‑2849399

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑