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%	109.8 / NA	31	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 (18/13);  total (18/13)

CGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAG  >  NZ_CP009273/1649389‑1649560                                                                                        |                                                                                     cGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGgaa                                                                                    <  1:715341/90‑1 (MQ=255)             tCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGgaaaa                                                                                  >  2:213464/1‑80 (MQ=255)             tCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGgaaaa                                                                                  <  1:213464/80‑1 (MQ=255)             tCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTg                                                                        >  1:360392/1‑90 (MQ=255)             tCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTg                                                                        >  2:771955/1‑90 (MQ=255)             tCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTg                                                                        >  1:569759/1‑90 (MQ=255)             tCGATTCCTTGCATCGCTTGACGTGATGCATGAAATCTACGCAACTGAGCTACCACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTg                                                                        <  2:210911/90‑1 (MQ=255)                aTTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATc                                                                     >  2:325183/1‑90 (MQ=255)                        cATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaa                                                             <  2:600647/90‑1 (MQ=255)                           cGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTTTAAAGATCGGAAAAAGCCGGAGTGATAAAAAAAAAAgg                                                          >  1:667759/1‑90 (MQ=255)                            gCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGc                                                         >  2:720685/1‑90 (MQ=255)                                   gTGATGCATGAAATCTACGCAACTGAGCTATTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATAtt                                                  <  1:854766/90‑1 (MQ=255)                                        gCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTgcgc                                             <  2:419909/90‑1 (MQ=255)                                        gCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTgcgc                                             <  1:765414/90‑1 (MQ=255)                                                  tACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAACCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGt                                   <  2:896355/90‑1 (MQ=255)                                                                actacCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGaa                     <  2:569759/90‑1 (MQ=255)                                                                     cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGa                >  2:44153/1‑90 (MQ=255)                                                                     cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGa                >  2:525803/1‑90 (MQ=255)                                                                     cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGa                >  2:590270/1‑90 (MQ=255)                                                                     cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGa                >  1:396677/1‑90 (MQ=255)                                                                     cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGa                >  1:592820/1‑90 (MQ=255)                                                                     cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCACTGTGAATGGTTGACAAAAGATGAAATAGa                >  2:903909/1‑90 (MQ=255)                                                                       tACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt              >  2:425214/1‑90 (MQ=255)                                                                       tACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt              <  2:360392/90‑1 (MQ=255)                                                                       tACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt              <  1:704459/90‑1 (MQ=255)                                                                       tACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt              <  1:574407/90‑1 (MQ=255)                                                                        aCAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt              <  2:709373/89‑1 (MQ=255)                                                                        aCAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt              >  1:709373/1‑89 (MQ=255)                                                                           aGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCt          >  2:268828/1‑90 (MQ=255)                                                                             tataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt              >  2:439526/1‑84 (MQ=255)                                                                             tataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt              <  1:439526/84‑1 (MQ=255)                                                                             tataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCttt        >  1:712887/1‑90 (MQ=255)                                                                                   gATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAg  >  2:739689/1‑90 (MQ=255)                                                                                     tCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGa                      <  2:294166/68‑1 (MQ=255)                                                                                        |                                                                                     CGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAG  >  NZ_CP009273/1649389‑1649560

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑