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%	147.6 / NA	53	E146* (GAG→TAG)	aroK	shikimate kinase AroK
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (25/28);  total (25/28)

ATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTA  >  NZ_CP009273/3511901‑3512073                                                                                        |                                                                                      aTTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTAtt                                                                                     <  1:809510/90‑1 (MQ=255) aTTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTAtt                                                                                     <  2:1234313/90‑1 (MQ=255) aTTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTAtt                                                                                     <  2:391389/90‑1 (MQ=255)       tGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACa                                                                               <  1:902998/90‑1 (MQ=255)          tttCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGAAATCTATTCATACAGCg                                                                            <  2:1242928/90‑1 (MQ=255)           ttCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCgg                                                                           >  2:1254962/1‑90 (MQ=255)             ccAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGAt                                                                         <  2:220058/90‑1 (MQ=255)                 cATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTgag                                                                     <  2:1482402/90‑3 (MQ=255)                      gAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCAt                                                                <  1:813873/90‑1 (MQ=255)                               ggTTTGCAACCGCTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACg                                                       <  2:244916/90‑1 (MQ=255)                               ggTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACg                                                       >  2:889447/1‑90 (MQ=255)                                gTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTgg                                                             >  1:1259510/1‑83 (MQ=255)                                gTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTgg                                                             <  2:1259510/83‑1 (MQ=255)                                gTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGc                                                      >  2:872758/1‑90 (MQ=255)                                  ttGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCtt                                                    >  1:478029/1‑90 (MQ=255)                                             ttAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCg                                                                     >  2:1058685/1‑62 (MQ=255)                                             ttAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCg                                                                     <  1:1058685/62‑1 (MQ=255)                                              tAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGTAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCAc                                        <  1:463804/90‑1 (MQ=255)                                              tAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATa                                                                                 >  2:974770/1‑49 (MQ=255)                                              tAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATa                                                                                 <  1:974770/49‑1 (MQ=255)                                               aGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCAcg                                       >  1:757233/1‑90 (MQ=255)                                                 cgcTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCAcgcg                                     >  2:1141435/1‑90 (MQ=255)                                                   cTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACgcggc                                   >  1:731690/1‑90 (MQ=255)                                                    tttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACgcggcg                                  >  2:443332/1‑90 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCAt                                                                >  1:604172/1‑59 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCAt                                                                <  2:604172/59‑1 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACgcggc                                   >  2:527068/1‑88 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACgcggc                                   <  1:527068/88‑1 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                                 <  2:765076/90‑1 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                                 <  1:330751/90‑1 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                                 <  2:285048/90‑1 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                                 <  2:478029/90‑1 (MQ=255)                                                     ttGATCATCAGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGACAACGCTTCCAGAACTTCACGcggcgg                                 <  1:1594056/90‑1 (MQ=255)                                                             caGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACg                                                       <  1:1014610/60‑1 (MQ=255)                                                             caGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACg                                                       >  2:1014610/1‑60 (MQ=255)                                                             caGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa                         <  1:1348457/90‑1 (MQ=255)                                                             caGTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa                         <  1:1254962/90‑1 (MQ=255)                                                               gTACGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACg                       >  1:1186462/1‑90 (MQ=255)                                                                 aCGAATGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTg                     >  1:1389686/1‑90 (MQ=255)                                                                    aaTGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                                 <  1:130829/75‑1 (MQ=255)                                                                    aaTGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGcggcgg                                 >  2:130829/1‑75 (MQ=255)                                                                    aaTGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa                         <  1:860275/83‑1 (MQ=255)                                                                    aaTGGTCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCaa                         >  2:860275/1‑83 (MQ=255)                                                                         tCACGTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACg             >  2:96885/1‑90 (MQ=255)                                                                             gTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCg         >  1:1552976/1‑90 (MQ=255)                                                                             gTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCg         >  1:826589/1‑90 (MQ=255)                                                                             gTCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCg         >  1:567342/1‑90 (MQ=255)                                                                              tCGGCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGt        <  2:1565673/90‑1 (MQ=255)                                                                                ggCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGgtt      >  2:1461474/1‑90 (MQ=255)                                                                                 gCAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGtttt     >  1:1481358/1‑90 (MQ=255)                                                                                  cAATCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGttttt    <  1:1526958/90‑1 (MQ=255)                                                                                   aaTCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGtttttt   >  1:1013831/1‑90 (MQ=255)                                                                                    aTCTATTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTa  <  1:1161688/90‑1 (MQ=255)                                                                                        |                                                                                      ATTAGTTGCTTTCCAGCATGTGAATAATCTGGTTTGCAACCACTTTAGCGCTTTGATCATCAGTACGAATGGTCACGTCGGCAATCTCTTCATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTA  >  NZ_CP009273/3511901‑3512073

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑