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%	83.4 / NA	26	E146* (GAG→TAG)	aroK	shikimate kinase AroK
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (13/13);  total (13/13)

GCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACG  >  NZ_CP009273/3511908‑3512062                                                                                 |                                                                           gCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAg                                                                   <  1:67384/90‑1 (MQ=255)                   aatCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGc                                                 >  1:61784/1‑90 (MQ=255)                      cTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCaa                                              >  2:253026/1‑90 (MQ=255)                        ggTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACg                                            <  1:386031/90‑1 (MQ=255)                        ggTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACg                                            <  2:447648/90‑1 (MQ=255)                             gCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTcc                                       >  2:480071/1‑90 (MQ=255)                              cAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTAtt                                                                          <  1:339386/54‑1 (MQ=255)                              cAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTAtt                                                                          >  2:339386/1‑54 (MQ=255)                                aCCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGa                                    <  2:489016/90‑1 (MQ=255)                                  cACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAAc                                  >  2:137788/1‑90 (MQ=255)                                    cTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACtt                                <  2:61784/90‑1 (MQ=255)                                            cTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTTGCCAACGCTTCCAGAACTTCACgcggc                        <  2:364626/90‑1 (MQ=255)                                              ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                      >  2:132150/1‑90 (MQ=255)                                              ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                      <  2:566581/90‑1 (MQ=255)                                              ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                      >  1:566581/1‑90 (MQ=255)                                                    atcaGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTc                <  1:395176/90‑1 (MQ=255)                                                    atcaGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTc                <  1:256107/90‑1 (MQ=255)                                                      caGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa              <  1:520970/90‑1 (MQ=255)                                                      caGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa              <  2:376419/90‑1 (MQ=255)                                                        gTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACg            >  1:397260/1‑90 (MQ=255)                                                        gTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACg            >  2:500019/1‑90 (MQ=255)                                                          aCGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTg          >  1:234776/1‑90 (MQ=255)                                                                  tCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACg  >  1:394674/1‑90 (MQ=255)                                                                  tCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACg  >  1:234882/1‑90 (MQ=255)                                                                     cGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAg                                     <  1:607163/52‑1 (MQ=255)                                                                     cGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAg                                     >  2:607163/1‑52 (MQ=255)                                                                                 |                                                                           GCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACG  >  NZ_CP009273/3511908‑3512062

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑