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%	221.6 / NA	63	Y292S (TAC→TCC)	waaL	O‑antigen ligase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (47/16);  total (47/16)

GAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGT  >  NZ_CP009273/3791096‑3791266                                                                                       |                                                                                     gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                   >  1:102315/1‑90 (MQ=255) gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                   >  1:1080302/1‑90 (MQ=255) gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                   >  1:379071/1‑90 (MQ=255)   aTCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGaaa                                                                                 >  2:428837/1‑90 (MQ=255)    tCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAt                                                                                <  2:525031/90‑1 (MQ=255)     cGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAtt                                                                               <  1:264221/90‑1 (MQ=255)      gCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTg                                                                              >  2:963331/1‑90 (MQ=255)      gCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTg                                                                              >  1:1150677/1‑90 (MQ=255)                aGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatat                                                                    <  2:300363/90‑1 (MQ=255)                aGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatat                                                                    <  2:418692/90‑1 (MQ=255)                 gCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatata                                                                   >  1:531063/1‑90 (MQ=255)                 gCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatata                                                                   >  1:555018/1‑90 (MQ=255)                 gCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatata                                                                   >  1:1155143/1‑90 (MQ=255)                 gCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatata                                                                   >  1:971260/1‑90 (MQ=255)                      aaaTGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAt                                                                                <  1:1152073/72‑1 (MQ=255)                      aaaTGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAt                                                                                >  2:1152073/1‑72 (MQ=255)                           aCTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGt                                                         >  2:666991/1‑90 (MQ=255)                           aCTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGt                                                         >  2:16429/1‑90 (MQ=255)                              tAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCAc                                                      >  1:1198202/1‑90 (MQ=255)                                    gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCttttt                                                >  1:726453/1‑90 (MQ=255)                                    gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCttttt                                                >  1:1012918/1‑90 (MQ=255)                                      tataCCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCa                                              >  2:174296/1‑90 (MQ=255)                                      tataCCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCa                                              >  1:101758/1‑90 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                        <  2:952577/90‑1 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                        >  2:1203955/1‑90 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                        >  2:1150043/1‑90 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                        <  2:102315/90‑1 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                      >  1:379862/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                      >  2:269359/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                      >  2:464667/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                      >  2:54156/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                      >  2:1156125/1‑90 (MQ=255)                                                       tgtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTc                             >  2:810636/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAtt                                                                               <  1:1229612/39‑1 (MQ=39)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAtt                                                                               >  2:1229612/1‑39 (MQ=39)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatatat                                                                  >  1:606587/1‑52 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatatat                                                                  <  2:606587/52‑1 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                            >  1:164544/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                            >  1:246113/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                            >  2:946727/1‑90 (MQ=255)                                                         ttACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAc                           >  1:482575/1‑90 (MQ=255)                                                         ttACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAc                           >  1:438874/1‑90 (MQ=255)                                                          tACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAcg                          >  2:1041560/1‑90 (MQ=255)                                                          tACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAcg                          >  1:9946/1‑90 (MQ=255)                                                           aCTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAcgc                         <  1:1150043/90‑1 (MQ=255)                                                              tCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCt                      >  2:654402/1‑90 (MQ=255)                                                                ccTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGa                    >  1:762216/1‑90 (MQ=255)                                                                  tAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGaaa                  >  2:517947/1‑90 (MQ=255)                                                                   aGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAg                 >  1:753113/1‑90 (MQ=255)                                                                    ggTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGt                >  2:705433/1‑90 (MQ=255)                                                                     gTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCAt                                             >  2:908784/1‑60 (MQ=255)                                                                     gTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCAt                                             <  1:908784/60‑1 (MQ=255)                                                                      tGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTAt              >  2:460010/1‑90 (MQ=255)                                                                       gCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATg             >  2:1228282/1‑90 (MQ=255)                                                                       gCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATg             <  2:120213/90‑1 (MQ=255)                                                                        cAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGa            >  2:149986/1‑90 (MQ=255)                                                                              tGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGt      >  1:90811/1‑90 (MQ=255)                                                                               ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCAt                                             >  1:708831/1‑50 (MQ=255)                                                                               ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCAt                                             <  2:708831/50‑1 (MQ=255)                                                                               ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGtt     >  1:391298/1‑90 (MQ=255)                                                                                gCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTa    <  1:946727/90‑1 (MQ=255)                                                                                gCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTa    <  2:379862/90‑1 (MQ=255)                                                                                  aaTGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGt  <  1:460010/90‑1 (MQ=255)                                                                                       |                                                                                     GAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGT  >  NZ_CP009273/3791096‑3791266

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑