Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,798,416	(T)8→7	coding (61/936 nt)	rfaS ←	LPS core biosynthesis protein RfaS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,798,409	0	T	.	100.0%	66.0 / NA	16	coding (68/936 nt)	rfaS	LPS core biosynthesis protein RfaS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (8/8);  total (8/8)

CAGCCATGCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAA  >  NZ_CP009273/3798321‑3798481                                                                                         |                                                                         cAGCCATGCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACtt                                                                         >  2:1169359/1‑90 (MQ=255)        gCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACtttttttca                                                                  >  1:771672/1‑88 (MQ=255)        gCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACtttttttca                                                                  >  2:498142/1‑88 (MQ=255)           ttATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGt                                                              >  1:906744/1‑90 (MQ=255)             atccatccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTAc                                                            >  2:938523/1‑90 (MQ=255)             atccatccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTAc                                                            >  2:772795/1‑90 (MQ=255)             atccatccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTAc                                                            >  2:735863/1‑90 (MQ=255)             atccatccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTAc                                                            <  2:1053891/90‑1 (MQ=255)             atccatccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTAc                                                            >  1:542575/1‑90 (MQ=255)                  tccCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAAt                                                       >  2:520982/1‑90 (MQ=255)                          tttGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTa                                               >  2:1069362/1‑90 (MQ=255)                          tttGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTa                                               <  2:574782/90‑1 (MQ=255)                                  ttttttATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATaa                                       <  2:1210720/90‑1 (MQ=255)                                           aaTCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAAcc                              >  2:662696/1‑90 (MQ=255)                                                            ttGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAaaataaat             <  2:757406/90‑1 (MQ=255)                                                               gtgtTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGt          <  1:772795/90‑1 (MQ=255)                                                                tgttgtTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTc         <  1:117403/90‑1 (MQ=255)                                                                      tataTTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCataata   <  1:938523/90‑1 (MQ=255)                                                                       atatTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCAtaataa  <  1:334828/90‑1 (MQ=255)                                                                                         |                                                                         CAGCCATGCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAA  >  NZ_CP009273/3798321‑3798481

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑