Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	60,340	T→C	M3V (ATG→GTG)	rluA ←	bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	60,340	0	T	C	100.0%	129.2 / NA	34	M3V (ATG→GTG)	rluA	bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (21/13);  total (21/13)

TGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCATCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCC  >  NZ_CP009273/60268‑60424                                                                         |                                                                                     tgACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGt                                                                    >  2:676154/1‑91 (MQ=255)       ccaTAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGa                                                              <  1:860563/91‑1 (MQ=255)               tGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTAc                                                      <  2:470986/91‑1 (MQ=255)               tGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTAc                                                      >  1:86919/1‑91 (MQ=255)                 gTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTcc                                                                      <  2:797510/73‑1 (MQ=255)                 gTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTcc                                                                      >  1:797510/1‑73 (MQ=255)                 gTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACaa                                                    >  1:194930/1‑91 (MQ=255)                 gTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACaa                                                    >  2:764254/1‑91 (MQ=255)                 gTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACaa                                                    >  1:822487/1‑91 (MQ=255)                 gTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACaa                                                    >  1:662928/1‑91 (MQ=255)                 gTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACaa                                                    >  1:313534/1‑91 (MQ=255)                  tCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAAc                                                   <  2:50364/91‑1 (MQ=255)                    aTCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGa                                                 >  1:156383/1‑91 (MQ=255)                            aCAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGc                                         <  2:451409/91‑1 (MQ=255)                              aGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAg                                       <  1:612260/91‑1 (MQ=255)                               ggATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAgg                                      >  1:341190/1‑91 (MQ=255)                               ggATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAgg                                      >  2:66966/1‑91 (MQ=255)                               ggATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAgg                                      >  2:486721/1‑91 (MQ=255)                               ggATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAgg                                      >  1:361510/1‑91 (MQ=255)                                gATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAggg                                     <  1:516031/91‑1 (MQ=255)                                  tAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGCTGCGTTACACCGCTCCCACGCAGGGCa                                   >  2:387579/1‑91 (MQ=255)                                      caaccaGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCa                               <  1:552287/91‑1 (MQ=255)                                       aaccaGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAg                              >  2:839098/1‑91 (MQ=255)                                         ccaGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAgcc                            >  1:49603/1‑89 (MQ=255)                                           aGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGc                          <  1:839098/91‑1 (MQ=255)                                           aGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGc                          <  1:741945/91‑1 (MQ=255)                                            gggTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGcc                         >  1:737761/1‑91 (MQ=255)                                               ttCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAc                      >  2:788668/1‑91 (MQ=255)                                                tCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAcc                     >  2:339557/1‑91 (MQ=255)                                                    gCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAcctgcc                 <  1:788668/91‑1 (MQ=255)                                                    gCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAcctgcc                 <  2:788009/91‑1 (MQ=255)                                                            ttGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAg         >  1:648124/1‑91 (MQ=255)                                                              gTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGc       <  2:584452/91‑1 (MQ=255)                                                                   tttCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTcc  >  2:514218/1‑91 (MQ=255)                                                                         |                                                                                     TGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCATCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCC  >  NZ_CP009273/60268‑60424

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑