Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,791,182	A→C	Y292S (TAC→TCC)	waaL →	O‑antigen ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,791,182	0	A	C	100.0%	67.4 / NA	22	Y292S (TAC→TCC)	waaL	O‑antigen ligase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (19/3);  total (19/3)

AGAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGT  >  NZ_CP009273/3791095‑3791266                                                                                        |                                                                                     aGAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCg                                                                                    >  1:411342/1‑90 (MQ=255)    aTCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGaaa                                                                                 >  2:445407/1‑90 (MQ=255)       gCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTg                                                                              >  1:181249/1‑90 (MQ=255)       gCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTg                                                                              >  1:166294/1‑90 (MQ=255)                  gCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatata                                                                   >  2:47448/1‑90 (MQ=255)                            aCTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGt                                                         >  2:30503/1‑90 (MQ=255)                             cTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTc                                                        >  2:280194/1‑90 (MQ=255)                                     gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAtt                                                                               >  2:37782/1‑59 (MQ=255)                                     gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAtt                                                                               <  1:37782/59‑1 (MQ=255)                                     gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCttttt                                                >  1:361531/1‑90 (MQ=255)                                             aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                        >  2:415933/1‑90 (MQ=255)                                             aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                        >  1:36394/1‑90 (MQ=255)                                               tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                      >  1:235/1‑90 (MQ=255)                                                         gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                            >  1:72981/1‑90 (MQ=255)                                                          ttACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAc                           >  2:60070/1‑90 (MQ=255)                                                              ttCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACgcgc                       <  2:166294/90‑1 (MQ=255)                                                               tCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCt                      >  1:342085/1‑90 (MQ=255)                                                               tCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATACATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCt                      >  2:123351/1‑90 (MQ=255)                                                                       tGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTAt              >  2:63406/1‑90 (MQ=255)                                                                              cTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTg       >  1:254370/1‑90 (MQ=255)                                                                                ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGtt     >  2:364888/1‑90 (MQ=255)                                                                                   aaTGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGt  <  2:108937/90‑1 (MQ=255)                                                                                        |                                                                                     AGAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGT  >  NZ_CP009273/3791095‑3791266

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑