Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,649,476	A→G	intergenic (‑78/+128)	rspA ← / ← ynfA	starvation‑sensing protein RspA/YnfA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,649,476	0	A	G	100.0%	86.6 / NA	25	intergenic (‑78/+128)	rspA/ynfA	starvation‑sensing protein RspA/YnfA family protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (15/10);  total (15/10)

ATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAG  >  NZ_CP009273/1649391‑1649560                                                                                      |                                                                                     aTCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGgaaaa                                                                                  <  2:77922/90‑1 (MQ=255)  tCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGgaaaaa                                                                                 >  2:631746/1‑90 (MQ=255)    ttCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGc                                                                               >  2:96980/1‑90 (MQ=255)     tCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGcc                                                                              >  2:239722/1‑90 (MQ=255)      cATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCg                                                                             <  2:346782/90‑1 (MQ=255)                      cATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaa                                                             <  2:519744/90‑1 (MQ=255)                      cATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaa                                                             <  2:245479/90‑1 (MQ=255)                              gTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGtat                                                     >  1:87742/1‑90 (MQ=255)                                      gCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTgcgc                                             <  2:401983/90‑1 (MQ=255)                                        aTGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaaa                                                            <  2:214618/73‑1 (MQ=255)                                        aTGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaaa                                                            >  1:214618/1‑73 (MQ=255)                                             aTCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAAt                                      <  1:184236/90‑1 (MQ=255)                                             aTCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAAt                                      <  2:565145/90‑1 (MQ=255)                                              tCTACACAACTGAGCTAGTACCATGCAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGGATATTTGCGCTGTGAATg                                     <  1:436822/90‑1 (MQ=255)                                                              actacCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGaa                     >  1:181674/1‑90 (MQ=255)                                                              actacCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGaa                     <  2:26153/90‑1 (MQ=255)                                                                   cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGa                >  1:60695/1‑90 (MQ=255)                                                                   cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGa                >  2:522407/1‑90 (MQ=255)                                                                    aTACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGaa               >  2:429284/1‑90 (MQ=255)                                                                         aGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCt          >  1:586012/1‑90 (MQ=255)                                                                         aGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCt          >  1:738475/1‑90 (MQ=255)                                                                           tataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGaaa                    <  2:317472/78‑1 (MQ=255)                                                                           tataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGaaa                    >  1:317472/1‑78 (MQ=255)                                                                           tataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCttt        >  1:78673/1‑90 (MQ=255)                                                                           tataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCttt        >  2:172960/1‑90 (MQ=255)                                                                            ataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCtttt       >  1:441699/1‑90 (MQ=255)                                                                                 gATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAg  >  2:165052/1‑90 (MQ=255)                                                                                      |                                                                                     ATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAG  >  NZ_CP009273/1649391‑1649560

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑