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%	81.8 / NA	27	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 (18/9);  total (18/9)

CGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTT  >  NZ_CP009273/1649389‑1649555                                                                                        |                                                                                cGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGgaa                                                                               <  1:458919/90‑1 (MQ=255)             tCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTg                                                                   >  1:199269/1‑90 (MQ=255)               gATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGAt                                                                 >  1:365540/1‑90 (MQ=255)                 ttCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAGGCCGGAGTGATca                                                               <  2:426944/90‑1 (MQ=255)                  tCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATcac                                                              <  1:154958/90‑1 (MQ=255)                    cTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaa                                                            >  1:255174/1‑90 (MQ=255)                     ttGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaa                                                           >  2:421560/1‑90 (MQ=255)                       gaaTCCCTTGCCGGGAGGCATGAAATTTCCCAAACTGAGATACTA‑CATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaa                                                        <  2:274085/88‑1 (MQ=255)                            gCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGc                                                    >  1:2496/1‑90 (MQ=255)                            gCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGc                                                    >  1:428685/1‑90 (MQ=255)                                 tCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAgg                                                     <  1:220372/84‑1 (MQ=255)                                 tCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAgg                                                     >  2:220372/1‑84 (MQ=255)                                   gTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATAtt                                             <  2:349038/90‑1 (MQ=255)                                     gATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTg                                           >  2:12654/1‑90 (MQ=255)                                        gCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTgcgc                                        <  1:229801/90‑1 (MQ=255)                                           tGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCtgt                                     >  2:22669/1‑90 (MQ=255)                                               aTCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAAt                                 <  2:22106/90‑1 (MQ=255)                                                             gCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGCGAATGGTTGACAAAAGAt                   >  1:366256/1‑90 (MQ=255)                                                                actacCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGaa                >  2:59092/1‑90 (MQ=255)                                                                 ctacCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGaaa               <  2:365540/90‑1 (MQ=255)                                                                     cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGa           >  2:4256/1‑90 (MQ=255)                                                                     cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGa           >  2:49591/1‑90 (MQ=255)                                                                      aTACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGaa          >  1:277992/1‑90 (MQ=255)                                                                      aTACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCAC‑AAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt         >  1:390224/1‑90 (MQ=255)                                                                          aaGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATAcc      >  1:172506/1‑90 (MQ=255)                                                                             tataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACaa                        <  2:108193/69‑1 (MQ=255)                                                                             tataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACaa                        >  1:108193/1‑69 (MQ=255)                                                                              ataAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCtttt  >  2:195607/1‑90 (MQ=255)                                                                                        |                                                                                CGATCTTCATGTTCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTT  >  NZ_CP009273/1649389‑1649555

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑