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%	15.8 / NA	5	coding (68/936 nt)	rfaS	LPS core biosynthesis protein RfaS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (2/3);  total (2/3)

CAGCCATGCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTC  >  NZ_CP009273/3798321‑3798490                                                                                         |                                                                                  cAGCCATGCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACtt                                                                                  >  1:182048/1‑90 (MQ=255)       tGCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACtttttttc                                                                            <  2:203960/90‑2 (MQ=255)                   cccTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATc                                                               >  1:163099/1‑90 (MQ=255)                                                    atatTTTTTTGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTtata                              <  1:247109/90‑1 (MQ=255)                                                           tttGGTGTTGTTATATTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTataaaataaa                       >  1:143240/1‑90 (MQ=255)                                                                      tataTTTTTTATCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCataata            <  2:143240/90‑1 (MQ=255)                                                                                aTCTTGTAC‑TTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTc  <  2:269407/90‑1 (MQ=255)                                                                                         |                                                                                  CAGCCATGCATTATCCATCCCTATTTTTGATATTTTTTTATTAATCCAGTTATATTTTTTTGGTGTTGTTATATTTTTTATCTTGTACTTTTTTTTCAGGTACTGAATCATTTTTAATTCATAATCTGCAACCCAATTTATAAAATAAATAGTCATAATAAAGTTAGTTC  >  NZ_CP009273/3798321‑3798490

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑