Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,433,524	G→A	L289F (CTC→TTC)	rpoA ←	DNA‑directed RNA polymerase subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,433,524	0	G	A	100.0%	204.8 / NA	52	L289F (CTC→TTC)	rpoA	DNA‑directed RNA polymerase subunit alpha
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (20/32);  total (20/32)

GCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCA  >  NZ_CP009273/3433440‑3433610                                                                                     |                                                                                       gcATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAAc                                                                                  <  2:88599/91‑1 (MQ=255) gcATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAAc                                                                                  <  2:82320/91‑1 (MQ=255)    tGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTc                                                                               <  2:440058/91‑1 (MQ=255)     gCCCAGAGACGTCCCACGGAAAGCCAGCACGTCTTTAATCTCAGTAAAAGA‑TTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCgg                                                                             <  1:773355/91‑1 (MQ=255)           agaCAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGc                                                                        <  2:299957/91‑1 (MQ=255)           agaCAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGc                                                                        <  1:526853/91‑1 (MQ=255)           agaCAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGc                                                                        <  2:806515/91‑1 (MQ=255)           agaCAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGc                                                                        <  2:446268/91‑1 (MQ=255)            gaCAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCt                                                                       <  2:686233/91‑1 (MQ=255)               aGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTa                                                                    >  1:490548/1‑91 (MQ=255)                gTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTAc                                                                   >  2:748084/1‑91 (MQ=255)                gTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTAc                                                                   >  1:241733/1‑91 (MQ=255)                gTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTAc                                                                   >  2:320360/1‑91 (MQ=255)                 tCCACGGGAAGCCAGAACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTAcc                                                                  <  1:646377/91‑1 (MQ=255)                    aCGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTAc                                                                          <  1:494354/80‑1 (MQ=255)                    aCGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTAc                                                                          >  2:494354/1‑80 (MQ=255)                      gggAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATc                                                             <  2:755146/91‑1 (MQ=255)                        gAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCAc                                                           <  2:880715/91‑1 (MQ=255)                          aGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTAcc                                                                  <  2:899439/82‑1 (MQ=255)                          aGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTAcc                                                                  >  1:899439/1‑82 (MQ=255)                          aGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATc                                                             <  2:1027507/87‑1 (MQ=255)                          aGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATc                                                             >  1:1027507/1‑87 (MQ=255)                           ggcAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGGACCAGATCACCGa                                                        <  1:351408/89‑1 (MQ=255)                              aGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGatat                                                     <  2:23018/91‑1 (MQ=255)                                 aCGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGt                                                  <  1:139942/91‑1 (MQ=255)                                    tCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGa                                               >  2:128690/1‑91 (MQ=255)                                            ctcAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCt                                       <  2:241733/91‑1 (MQ=255)                                              cAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGc                                                                        <  2:520168/56‑1 (MQ=255)                                              cAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGc                                                                        >  1:520168/1‑56 (MQ=255)                                              cAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATc                                                             >  1:463615/1‑67 (MQ=255)                                              cAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATc                                                             <  2:463615/67‑1 (MQ=255)                                              cAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGatat                                                     >  1:1043668/1‑75 (MQ=255)                                              cAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGatat                                                     <  2:1043668/75‑1 (MQ=255)                                              cAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGc                                     >  1:172518/1‑91 (MQ=255)                                              cAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGc                                     >  2:405373/1‑91 (MQ=255)                                               aGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCt                                    >  2:641328/1‑91 (MQ=255)                                                   agagATTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTaa                                <  2:402189/91‑1 (MQ=255)                                                     agaTTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAgg                              <  1:748084/91‑1 (MQ=255)                                                     agaTTTTTTACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAgg                              <  1:320360/91‑1 (MQ=255)                                                        ttttttACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAg                           <  2:616906/91‑1 (MQ=255)                                                        ttttttACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAg                           >  2:153700/1‑91 (MQ=255)                                                        ttttttACCAAGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAg                           >  2:329436/1‑91 (MQ=255)                                                                 aaGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATa                                             >  2:506195/1‑64 (MQ=255)                                                                 aaGGTTAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATa                                             <  1:506195/64‑1 (MQ=255)                                                                      tAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGt                                                  <  1:311344/54‑1 (MQ=255)                                                                      tAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGt                                                  >  2:311344/1‑54 (MQ=255)                                                                      tAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCt                                       >  1:364523/1‑65 (MQ=255)                                                                      tAGGCGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCt                                       <  2:364523/65‑1 (MQ=255)                                                                          cGTTTTAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTc         <  1:641328/91‑1 (MQ=255)                                                                             tttAAGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAAt      >  2:661626/1‑91 (MQ=255)                                                                                 aGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCa  <  1:661626/91‑1 (MQ=255)                                                                                 aGGAACTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCa  <  1:128690/91‑1 (MQ=255)                                                                                     |                                                                                       GCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCA  >  NZ_CP009273/3433440‑3433610

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑