Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,593,877	T→C	A89A (GCA→GCG)	rpoH ←	RNA polymerase sigma factor RpoH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,593,877	0	T	C	100.0%	134.8 / NA	36	A89A (GCA→GCG)	rpoH	RNA polymerase sigma factor RpoH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (16/20);  total (16/20)

AACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACTGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAAC  >  NZ_CP009273/3593793‑3593960                                                                                     |                                                                                    aaCGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTtc                                                                               >  1:485862/1‑91 (MQ=255)     tATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTtcatca                                                                           >  2:297916/1‑91 (MQ=255)        tCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCGGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGc                                                                        <  2:458704/91‑1 (MQ=255)        tCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGc                                                                        <  2:678163/91‑1 (MQ=255)        tCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGc                                                                        <  2:167617/91‑1 (MQ=255)            ggATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGAt                                                                    >  1:436849/1‑91 (MQ=255)              aTCTCTGCTTTGATCCAGTGAACGGCGAAGGAGCCCAGGCGCACACCCCCTTCCGGGTTGCACCGGCGCCCCGCTTTCCTCCGGCCGATGt                                                                  >  2:76552/1‑91 (MQ=255)                  ctGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTAcc                                                              >  1:549832/1‑91 (MQ=255)                            ccAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATc                                                    >  1:301111/1‑91 (MQ=255)                              aGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCaa                                                  >  2:274828/1‑91 (MQ=255)                              aGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCaa                                                  >  2:44949/1‑91 (MQ=255)                                 gAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGa                                                                     <  1:324810/69‑1 (MQ=255)                                 gAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGa                                                                     >  2:324810/1‑69 (MQ=255)                                   aCGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCg                                             >  1:199112/1‑91 (MQ=255)                                      gCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCt                                          <  2:485862/91‑1 (MQ=255)                                      gCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCt                                          <  2:390502/91‑1 (MQ=255)                                            gagaCCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCa                                    <  1:161006/91‑1 (MQ=255)                                                 cAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCa                               <  2:199112/91‑1 (MQ=255)                                                      gccgacCCGCTTCCGGGTTGAAACGGCGCGCCGCTTTCATCAGGCCGATGTTACCTTCCTGGATCAAATCCGCCTGTGGCAGGCCATAGcc                          <  2:641516/87‑1 (MQ=38)                                                        acacCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCg                        >  1:434657/1‑91 (MQ=255)                                                        acacCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCg                        >  2:723988/1‑91 (MQ=255)                                                         cacCCACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGc                       <  1:339696/91‑1 (MQ=255)                                                           cccACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGctt                     <  1:683967/91‑3 (MQ=255)                                                           cccACTTCCGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCAt                     <  1:154914/91‑1 (MQ=255)                                                                ttCCGGGTTGAAACGACGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTa                <  2:367162/91‑1 (MQ=255)                                                                  ccGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACg              <  1:777728/91‑1 (MQ=255)                                                                   cGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAAt                                                     <  1:539299/51‑1 (MQ=255)                                                                   cGGGTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAAt                                                     >  2:539299/1‑51 (MQ=255)                                                                    gggTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAg            <  2:436849/91‑1 (MQ=255)                                                                    gggTTGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAg            <  1:276876/91‑1 (MQ=255)                                                                       ttGAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCaa         >  1:725872/1‑91 (MQ=255)                                                                         gAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGcc                                           <  2:116741/55‑1 (MQ=255)                                                                         gAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGcc                                           >  1:116741/1‑55 (MQ=255)                                                                         gAAACGGCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAata       <  1:217452/91‑1 (MQ=255)                                                                              ggCGCACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGaac  <  1:451839/91‑1 (MQ=255)                                                                               gcgcACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGa    >  1:54035/1‑88 (MQ=255)                                                                               gcgcACCGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGa    <  2:54035/88‑1 (MQ=255)                                                                                     |                                                                                    AACGTATTCGTGGATCTCTGCTTTGATCCAGTGAACGGCGAAGGAGACCAGGCGCACACCCACTTCCGGGTTGAAACGGCGCACTGCTTTCATCAGGCCGATGTTACCTTCCTGAATCAAATCCGCCTGTGGCAGGCCATAGCCCGCATAATTACGAGCAATATGAAC  >  NZ_CP009273/3593793‑3593960

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑