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%	62.8 / NA	20	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 (11/9);  total (11/9)

TCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCT  >  NZ_CP009273/1649401‑1649552                                                                            |                                                                             tCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTg                                                                >  1:286960/1‑90 (MQ=255)   gATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGAt                                                              >  1:421443/1‑90 (MQ=255)   gATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGAt                                                              >  1:456490/1‑90 (MQ=255)         ttGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaa                                                        >  1:221715/1‑90 (MQ=255)         ttGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaa                                                        >  1:93765/1‑90 (MQ=255)             aTCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACaaaaaaa                                                    <  1:15394/90‑1 (MQ=255)               cGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAgg                                                  <  1:272571/90‑1 (MQ=255)                gCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGc                                                 >  1:160129/1‑90 (MQ=255)                gCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGc                                                 >  1:294904/1‑90 (MQ=255)                            gCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTgcgc                                     <  1:84091/90‑1 (MQ=255)                            gCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTgcgc                                     <  2:469985/90‑1 (MQ=255)                                 aaaTCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGa                                <  2:456490/90‑1 (MQ=255)                                                         cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGa              <  1:513652/84‑1 (MQ=255)                                                         cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGa              >  2:513652/1‑84 (MQ=255)                                                         cATACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGa        >  2:274732/1‑90 (MQ=255)                                                          aTACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGaa       >  2:170628/1‑90 (MQ=255)                                                           tACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt      <  2:221715/90‑1 (MQ=255)                                                           tACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt      <  2:421443/90‑1 (MQ=255)                                                           tACAAGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAAt      <  2:93765/90‑1 (MQ=255)                                                               aGTATAAAGATCGGAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAGTACCt  >  1:32391/1‑90 (MQ=255)                                                                            |                                                                             TCGATTCCTTGCATCGCTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCT  >  NZ_CP009273/1649401‑1649552

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑