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	96.8%	99.9 / ‑3.9	31	Y292S (TAC→TCC)	waaL	O‑antigen ligase
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base C (23/7);  total (24/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

GAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTT  >  NZ_CP009273/3791096‑3791263                                                                                       |                                                                                  gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                >  1:306393/1‑90 (MQ=255) gAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGa                                                                                >  1:7325/1‑90 (MQ=255)   aTCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGaaa                                                                              >  2:335353/1‑90 (MQ=255)    tCGCTGTAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAAt                                                                             <  1:300353/90‑1 (MQ=255)                aGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatat                                                                 <  2:459646/90‑1 (MQ=255)                 gCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatata                                                                >  1:432033/1‑90 (MQ=255)                 gCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAatata                                                                >  1:401261/1‑90 (MQ=255)                                    gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCttttt                                             >  1:181073/1‑90 (MQ=255)                                     ttATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTc                                            >  1:19598/1‑90 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                     <  2:7325/90‑1 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                     >  1:441807/1‑90 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                     >  2:182651/1‑90 (MQ=255)                                            aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa                                     >  2:428780/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                   >  1:460301/1‑90 (MQ=255)                                              tGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATc                                   >  1:54214/1‑90 (MQ=255)                                                 tAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATcagc                                <  2:181073/90‑1 (MQ=255)                                                     aGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCagag                            >  2:394806/1‑90 (MQ=255)                                                       tgtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTc                          <  2:54214/90‑1 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                         >  2:226075/1‑90 (MQ=255)                                                        gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAACATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa                         >  2:25140/1‑90 (MQ=255)                                                         ttACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAc                        <  2:460301/90‑1 (MQ=255)                                                          tACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCAcg                       >  1:372531/1‑90 (MQ=255)                                                              tCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCt                   >  1:434858/1‑90 (MQ=255)                                                              tCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCt                   >  1:23197/1‑90 (MQ=255)                                                                ccTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGa                 >  1:429231/1‑90 (MQ=255)                                                                ccTAGGTGCAAGACTGCCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGa                 >  2:481419/1‑90 (MQ=255)                                                                    ggTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGt             >  1:431289/1‑90 (MQ=255)                                                                       gCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATg          <  2:309917/90‑1 (MQ=255)                                                                              tGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGt   >  2:431114/1‑90 (MQ=255)                                                                              tGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGt   >  1:374886/1‑90 (MQ=255)                                                                               ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGtt  >  2:27793/1‑90 (MQ=255)                                                                                       |                                                                                  GAATCGCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTT  >  NZ_CP009273/3791096‑3791263

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: ‑