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%	105.0 / NA	30	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 (15/15);  total (15/15)

TCTTTGTGCTCTTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCATCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCACGAA  >  NZ_CP009273/60216‑60473                                                                                                                             |                                                                                                                                      tCTTTGTGCTCTTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCgg                                                                                                                           <  1:331463/137‑1 (MQ=255)     tgtgCTCTTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTc                                                                                                                        <  1:397135/136‑1 (MQ=255)         ctctTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTAc                                                                                                                  <  1:270883/138‑1 (MQ=255)           ctTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGa                                                                                                               >  1:22098/1‑139 (MQ=255)            ttCCATACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTg                                                                                                                <  1:439075/137‑1 (MQ=255)                     acCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACaa                                                                                                     <  2:199178/139‑1 (MQ=255)                     acCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACaa                                                                                                     <  1:16775/139‑1 (MQ=255)                      cccGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAAc                                                                                                    >  2:264468/1‑139 (MQ=255)                      cccGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATACGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAAc                                                                                                    >  2:222018/1‑139 (MQ=255)                                acaacaAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTg                                                                                                                <  1:185214/117‑1 (MQ=255)                                acaacaAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTg                                                                                                                >  2:185214/1‑117 (MQ=255)                                acaacaAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACg                                                                                           >  2:201565/1‑138 (MQ=255)                                                cTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGcc                                                                          <  2:22098/139‑1 (MQ=255)                                                       accaccATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAcctgc                                                                   <  1:264468/139‑1 (MQ=255)                                                                   tGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGc                                                        <  1:201565/138‑1 (MQ=255)                                                                        aTCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCgg                                                                                                                           <  2:296605/66‑1 (MQ=255)                                                                        aTCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCgg                                                                                                                           >  1:296605/1‑66 (MQ=255)                                                                         tCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCAt                                                 >  1:198426/1‑139 (MQ=255)                                                                                    gATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGAc                                      >  1:20373/1‑139 (MQ=255)                                                                                    gATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGAc                                      >  1:371759/1‑139 (MQ=255)                                                                                       aaccaaccAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGt                                   >  1:436019/1‑139 (MQ=255)                                                                                        accaaccaGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGtt                                  >  2:67456/1‑139 (MQ=255)                                                                                         ccaaccaGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTg                                 <  1:67456/139‑1 (MQ=255)                                                                                                    tCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAgg                                                         >  1:333291/1‑104 (MQ=255)                                                                                                    tCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAgg                                                         <  2:333291/104‑1 (MQ=255)                                                                                                           gTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGt               >  2:381430/1‑139 (MQ=255)                                                                                                                     gTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCAc     <  2:198426/139‑1 (MQ=255)                                                                                                                        ttCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCACg    >  1:366435/1‑137 (MQ=255)                                                                                                                        ttCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCACg    <  2:366435/137‑1 (MQ=255)                                                                                                                        ttCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCACGaa  >  1:295247/1‑139 (MQ=255)                                                                                                                             |                                                                                                                                      TCTTTGTGCTCTTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCATCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCACGAA  >  NZ_CP009273/60216‑60473

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑