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%	299.3 / NA	81	Y292S (TAC→TCC)	waaL	O‑antigen ligase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (56/25);  total (56/25)

GAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGT  >  NZ_CP009273/3791096‑3791266                                                                                       |                                                                                     gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                   >  1:846351/1‑90 (MQ=255) gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                   >  1:763981/1‑90 (MQ=255) gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                   >  1:677877/1‑90 (MQ=255) gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                   >  1:333478/1‑90 (MQ=255) gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                   >  1:591539/1‑90 (MQ=255)    tCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAt                                                                                <  1:82136/90‑1 (MQ=255)    tCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAt                                                                                <  2:244049/90‑1 (MQ=255)      gCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAtt                                                                               >  2:519277/1‑89 (MQ=255)      gCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAtt                                                                               <  1:519277/89‑1 (MQ=255)      gCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTg                                                                              >  1:223797/1‑90 (MQ=255)      gCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTg                                                                              >  1:747864/1‑90 (MQ=255)      gCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTg                                                                              >  1:70874/1‑90 (MQ=255)           aaTGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTa                                                                         >  1:35686/1‑90 (MQ=255)               aaGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAata                                                                     >  2:550535/1‑90 (MQ=255)                aGCATTAAATTACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatat                                                                    <  2:846351/90‑1 (MQ=255)                aGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatat                                                                    <  2:34201/90‑1 (MQ=255)                aGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAAACTGGCAATGTCCGAAATTGGTTTAAatat                                                                    <  2:64671/90‑1 (MQ=255)                 gCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatata                                                                   >  2:124843/1‑90 (MQ=255)                   aTTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATAtt                                                                 >  2:130651/1‑90 (MQ=255)                      aaaTGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCAt                                                              <  2:638161/90‑1 (MQ=255)                      aaaTGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCAt                                                              >  2:417461/1‑90 (MQ=255)                        aTGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATaa                                                            <  2:115104/90‑1 (MQ=255)                        aTGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATaa                                                            >  2:492153/1‑90 (MQ=255)                        aTGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATaa                                                            <  1:287218/90‑1 (MQ=255)                           aCTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGt                                                         >  1:569067/1‑90 (MQ=255)                           aCTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGt                                                         >  2:803781/1‑90 (MQ=255)                           aCTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGt                                                         >  2:756790/1‑90 (MQ=255)                              tAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCAc                                                      >  2:323968/1‑90 (MQ=255)                                aaCAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCt                                                    >  2:508484/1‑90 (MQ=255)                                    gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAtt                                                                               >  2:320640/1‑59 (MQ=255)                                    gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAtt                                                                               <  1:320640/59‑1 (MQ=255)                                      tataCCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCa                                              >  1:319347/1‑90 (MQ=255)                                      tataCCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCa                                              >  1:863760/1‑90 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCa                                                               >  1:522372/1‑67 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCa                                                               <  2:522372/67‑1 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                        >  2:316726/1‑90 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                        >  2:446545/1‑90 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                        <  2:591539/90‑1 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAt                                                                                >  2:911417/1‑48 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAt                                                                                <  1:911417/48‑1 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCttttt                                                <  1:749438/80‑1 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCttttt                                                >  2:749438/1‑80 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                      >  2:601132/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                      >  2:410597/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                      >  1:474773/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                      >  2:822208/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                      <  1:813461/90‑1 (MQ=255)                                                 tAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATcagc                                   <  1:316726/90‑1 (MQ=255)                                                       tgtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTc                             >  1:772312/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGGAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                            >  2:522610/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatat                                                                    <  1:228503/50‑1 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatat                                                                    >  2:228503/1‑50 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                            >  1:793402/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                            >  2:878731/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                            >  2:359001/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                            >  1:594277/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                            >  2:49481/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                            >  1:685262/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGACa                            >  1:706004/1‑90 (MQ=255)                                                         ttACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAc                           <  1:190233/90‑1 (MQ=255)                                                         ttACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAc                           >  2:899569/1‑90 (MQ=255)                                                         ttACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAc                           >  1:72103/1‑90 (MQ=255)                                                             ttCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACgcgc                       <  1:544637/90‑1 (MQ=255)                                                              tCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCt                      >  2:183391/1‑90 (MQ=255)                                                                ccTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCttttt                                                >  1:205751/1‑62 (MQ=255)                                                                ccTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCttttt                                                <  2:205751/62‑1 (MQ=255)                                                                ccTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGa                    >  1:901774/1‑90 (MQ=255)                                                                 cTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGaa                   <  1:63728/90‑1 (MQ=255)                                                                     gTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTa               <  2:594277/90‑1 (MQ=255)                                                                      tGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTAt              <  2:772312/90‑1 (MQ=255)                                                                        cAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGa            >  2:310380/1‑90 (MQ=255)                                                                             cTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCtttt                                                 <  2:310205/48‑1 (MQ=255)                                                                             cTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCtttt                                                 >  1:310205/1‑48 (MQ=255)                                                                             cTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTg       >  1:899915/1‑90 (MQ=255)                                                                              tGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGt      >  2:14758/1‑90 (MQ=255)                                                                              tGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGt      >  2:416577/1‑90 (MQ=255)                                                                               ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGtt     >  1:340811/1‑90 (MQ=255)                                                                               ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGtt     >  1:745719/1‑90 (MQ=255)                                                                               ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGtt     >  2:160299/1‑90 (MQ=255)                                                                               ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGtt     >  1:735564/1‑90 (MQ=255)                                                                                  aaTGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGt  <  1:508484/90‑1 (MQ=255)                                                                                       |                                                                                     GAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGT  >  NZ_CP009273/3791096‑3791266

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑