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%	98.1 / NA	30	Y292S (TAC→TCC)	waaL	O‑antigen ligase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (26/4);  total (26/4)

GAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTT  >  NZ_CP009273/3791096‑3791263                                                                                       |                                                                                  gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                >  1:150846/1‑90 (MQ=255) gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                >  1:325970/1‑90 (MQ=255)   aTCGCTATAATGAAGCATTAAATGACTTAAGCAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGaaa                                                                              >  1:505863/1‑90 (MQ=255)   aTCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGaaa                                                                              >  2:425771/1‑90 (MQ=255)   aTCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGaaa                                                                              >  1:68568/1‑90 (MQ=255)      gCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTg                                                                           >  1:461662/1‑90 (MQ=255)                           aCTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGt                                                      >  1:267495/1‑90 (MQ=255)                                   aGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCtttt                                              <  1:179462/90‑1 (MQ=255)                                    gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCa                                                            <  2:336935/75‑1 (MQ=255)                                    gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCa                                                            >  1:336935/1‑75 (MQ=255)                                    gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCttttt                                             >  1:402860/1‑90 (MQ=255)                                     ttATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTc                                            >  1:453203/1‑90 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                     >  1:348246/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                   >  2:474992/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                   >  1:315590/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                   >  1:465550/1‑90 (MQ=255)                                                  aaTAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATcagca                               >  1:62851/1‑90 (MQ=255)                                                  aaTAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATcagca                               >  2:74584/1‑90 (MQ=255)                                                      gtgtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGt                           >  1:489588/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                     <  1:514178/78‑1 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                     >  2:514178/1‑78 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                         >  2:265068/1‑90 (MQ=255)                                                         ttACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAc                        >  1:361889/1‑90 (MQ=255)                                                           aCTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAcgc                      <  2:267495/90‑1 (MQ=255)                                                                ccTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGa                 >  1:477750/1‑90 (MQ=255)                                                                ccTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGa                 >  2:172095/1‑90 (MQ=255)                                                                     gTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTa            >  2:469888/1‑90 (MQ=255)                                                                             cTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTg    >  2:166922/1‑90 (MQ=255)                                                                               ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGtt  >  2:35685/1‑90 (MQ=255)                                                                               ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGtt  >  1:429327/1‑90 (MQ=255)                                                                                       |                                                                                  GAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTT  >  NZ_CP009273/3791096‑3791263

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑