Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,511,988	C→A	E146* (GAG→TAG)	aroK ←	shikimate kinase AroK

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,511,988	0	C	A	100.0%	112.5 / NA	31	E146* (GAG→TAG)	aroK	shikimate kinase AroK
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (18/13);  total (18/13)

ATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTT  >  NZ_CP009273/3511901‑3512069                                                                                        |                                                                                  aTTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTAtt                                                                                 <  2:338425/90‑1 (MQ=255)           ttCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCgg                                                                       >  2:678628/1‑90 (MQ=255)             ccAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGAt                                                                     <  2:374530/90‑1 (MQ=255)                  aTGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGt                                                                >  1:891026/1‑90 (MQ=255)                                                  gcTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGa                                                                      <  2:701764/52‑1 (MQ=255)                                                  gcTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGa                                                                      >  1:701764/1‑52 (MQ=255)                                                   cTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACgcggc                               <  2:217285/90‑1 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                             >  2:75078/1‑90 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                             >  2:751112/1‑90 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                             >  2:441666/1‑90 (MQ=255)                                                             caGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa                     >  1:385374/1‑90 (MQ=255)                                                             caGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa                     <  1:220790/90‑1 (MQ=255)                                                             caGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa                     <  1:461434/90‑1 (MQ=255)                                                               gTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                             <  2:451565/80‑1 (MQ=255)                                                               gTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                             >  1:451565/1‑80 (MQ=255)                                                               gTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTc                       <  1:831118/86‑1 (MQ=255)                                                               gTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTc                       >  2:831118/1‑86 (MQ=255)                                                               gTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACg                   >  1:421597/1‑90 (MQ=255)                                                                    aaTGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa                     <  1:83288/83‑1 (MQ=255)                                                                    aaTGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa                     >  2:83288/1‑83 (MQ=255)                                                                    aaTGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTgcag              >  1:743778/1‑90 (MQ=255)                                                                       ggTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCaa           >  1:340010/1‑90 (MQ=255)                                                                       ggTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCaa           >  2:394162/1‑90 (MQ=255)                                                                         tCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa                     >  2:123583/1‑78 (MQ=255)                                                                         tCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa                     <  1:123583/78‑1 (MQ=255)                                                                         tCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACg         >  2:857003/1‑90 (MQ=255)                                                                         tCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACg         >  2:613308/1‑90 (MQ=255)                                                                           aCGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACggg       <  2:623770/90‑1 (MQ=255)                                                                            cGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCAcgc                                  <  2:21472/62‑1 (MQ=255)                                                                            cGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCAcgc                                  >  1:21472/1‑62 (MQ=255)                                                                                ggCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGttt  <  2:603544/90‑1 (MQ=255)                                                                                        |                                                                                  ATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTT  >  NZ_CP009273/3511901‑3512069

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑