Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,931,448	G→T	L265F (TTG→TTT)	rbsK →	ribokinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,931,448	0	G	T	90.0%	122.9 / 7.4	40	L265F (TTG→TTT)	rbsK	ribokinase
Reads supporting (aligned to +/- strand):  ref base G (3/1);  new base T (18/18);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 6.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.49e-01

GGTCAGCGCGTTCCTGGATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTGCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACAACC  >  NZ_CP009273/3931362‑3931531                                                                                       |                                                                                    ggTCAGCGCGTTCCTGGATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTg                                                                                  >  2:114597/1‑90 (MQ=255)      gcgcGTTCCTGGATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGgaaga                                                                             >  1:380420/1‑90 (MQ=255)      gcgcGTTCCTGGATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGgaaga                                                                             >  2:625650/1‑90 (MQ=255)      gcgcGTTCCTGGATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTGCTGgaaga                                                                             >  2:274509/1‑90 (MQ=255)           ttCCTGGATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAAc                                                                        >  2:79794/1‑90 (MQ=255)                  aTTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGcc                                                                 <  1:509210/90‑1 (MQ=255)                      cGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTGCTGGAAGAAAAACCATTGCCagag                                                             <  1:274509/90‑1 (MQ=255)                       gggTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAgg                                                            >  2:158045/1‑90 (MQ=255)                                      aTACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGccc                                             <  1:62784/90‑1 (MQ=255)                                            ttGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCAtgctg                                       >  2:831828/1‑90 (MQ=255)                                            ttGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCAtgctg                                       >  1:242038/1‑90 (MQ=255)                                            ttGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCAtgctg                                       >  2:101216/1‑90 (MQ=255)                                            ttGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCAtgctg                                       >  2:237001/1‑90 (MQ=255)                                            ttGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCAtgctg                                       >  1:598097/1‑90 (MQ=255)                                            ttGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTGCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCAtgctg                                       >  2:663965/1‑90 (MQ=255)                                                         tACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGc                          >  2:831006/1‑90 (MQ=255)                                                         tACCTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGc                          >  1:284030/1‑90 (MQ=255)                                                            cTTTAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGt                       <  2:284030/90‑1 (MQ=255)                                                              ttAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTaa                     <  2:365981/90‑1 (MQ=255)                                                              ttAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTaa                     <  1:133532/90‑1 (MQ=255)                                                              ttAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTaa                     >  2:679060/1‑90 (MQ=255)                                                              ttAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTaa                     <  2:840922/90‑1 (MQ=255)                                                              ttAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTaa                     <  1:335610/90‑1 (MQ=255)                                                              ttAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTaa                     <  1:79794/90‑1 (MQ=255)                                                              ttAACGGTGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTaa                     <  1:754124/90‑1 (MQ=255)                                                                     tGCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTaa              >  1:651457/1‑90 (MQ=255)                                                                     tGCGTTAATCACGGCATTGCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTaa              >  1:86826/1‑90 (MQ=255)                                                                      gCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTaaa             <  1:184237/90‑1 (MQ=255)                                                                      gCGTTAATCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTaaa             <  1:51509/90‑1 (MQ=255)                                                                             tCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGcac      <  2:216410/90‑1 (MQ=255)                                                                             tCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGcac      <  2:43474/90‑1 (MQ=255)                                                                             tCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGcac      <  2:305479/90‑1 (MQ=255)                                                                             tCACGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGcac      <  1:831828/90‑1 (MQ=255)                                                                               aCGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACaa    <  1:406763/90‑1 (MQ=255)                                                                               aCGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACaa    <  1:10055/90‑1 (MQ=255)                                                                                cGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACAAc   >  2:566562/1‑90 (MQ=255)                                                                                cGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACAAc   >  2:698045/1‑90 (MQ=255)                                                                                cGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACAAc   >  1:315738/1‑90 (MQ=255)                                                                                cGGCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACAAc   >  2:213599/1‑90 (MQ=255)                                                                                 ggCATTTCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACAAcc  <  2:89823/90‑1 (MQ=255)                                                                                       |                                                                                    GGTCAGCGCGTTCCTGGATTCCGGGTGCAGGCTGTCGATACCATTGCTGCCGGAGATACCTTTAACGGTGCGTTAATCACGGCATTGCTGGAAGAAAAACCATTGCCAGAGGCGATTCGTTTTGCCCATGCTGCCGCTGCGATTGCCGTAACACGTAAAGGCGCACAACC  >  NZ_CP009273/3931362‑3931531

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑