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%	179.0 / NA	51	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 (31/20);  total (31/20)

ATCACGCTGTCTTTGTGCTCTTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCATCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCACGAAT  >  NZ_CP009273/60207‑60474                                                                                                                                      |                                                                                                                                       atcaCGCTGTCTTTGTGCTCTTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCa                                                                                                                                   >  2:37969/1‑139 (MQ=255)          tCTTTGTGCTCTTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCt                                                                                                                          >  1:319831/1‑139 (MQ=255)                tgCTCTTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTa                                                                                                                    >  2:490575/1‑139 (MQ=255)                    ctTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGa                                                                                                                >  2:28715/1‑139 (MQ=255)                     ttCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTg                                                                                                                 <  2:122991/137‑1 (MQ=255)                               tccGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAAc                                                                                                     >  1:318559/2‑139 (MQ=255)                               cccGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAAc                                                                                                     >  2:355382/1‑139 (MQ=255)                               cccGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAAc                                                                                                     >  2:508660/1‑139 (MQ=255)                                         acaacaAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACg                                                                                            >  2:360535/1‑138 (MQ=255)                                         acaacaAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACg                                                                                            >  2:427500/1‑138 (MQ=255)                                         acaacaAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACg                                                                                            <  1:28715/138‑1 (MQ=255)                                          caacaaACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCa                                                                                          <  1:355382/139‑1 (MQ=255)                                              aaaCCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAggg                                                                                       >  1:299097/1‑138 (MQ=255)                                                   gCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATc                                                                                   >  2:49190/1‑137 (MQ=255)                                                       gccTTGTTGACCACCATAATATGGTCATCCTGATACAGAATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCCCCCCCACTTTCGGCTCCTTTACTGATGCATTACAACGATCAAACGCAGGGCATCCAGACg                                                                             <  2:181653/137‑1 (MQ=255)                                                                accaccATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAcctgc                                                                    <  1:427500/139‑1 (MQ=255)                                                                accaccATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACAATCAAACGCAGGGCATCCAGACGCCAAcctgc                                                                    <  1:503484/139‑1 (MQ=255)                                                                            tGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGc                                                         <  2:280130/138‑1 (MQ=255)                                                                               tCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACaa                                                                                                      <  2:554780/90‑1 (MQ=255)                                                                               tCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACaa                                                                                                      >  1:554780/1‑90 (MQ=255)                                                                               tCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTc                                                     >  2:168973/1‑139 (MQ=255)                                                                               tCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTc                                                     >  2:547393/1‑139 (MQ=255)                                                                               tCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTc                                                     >  1:394354/1‑139 (MQ=255)                                                                               tCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTc                                                     >  1:382075/1‑139 (MQ=255)                                                                                cATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTc                                                     >  1:148444/1‑138 (MQ=255)                                                                                 aTCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCa                                                   <  2:215491/139‑1 (MQ=255)                                                                                  tCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCgg                                                                                                                            >  1:78804/1‑65 (MQ=255)                                                                                  tCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCgg                                                                                                                            <  2:78804/65‑1 (MQ=255)                                                                                  tCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAc                                                                        >  2:238002/1‑117 (MQ=255)                                                                                  tCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAc                                                                        <  1:238002/117‑1 (MQ=255)                                                                                  tCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCAt                                                  >  2:505227/1‑139 (MQ=255)                                                                                             gATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAcctgc                                                                    >  2:140891/1‑110 (MQ=255)                                                                                             gATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAcctgc                                                                    <  1:140891/110‑1 (MQ=255)                                                                                             gATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGAc                                       >  2:500226/1‑139 (MQ=255)                                                                                             gATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGAc                                       >  2:86961/1‑139 (MQ=255)                                                                                             gATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGAc                                       >  2:292664/1‑139 (MQ=255)                                                                                             gATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGAc                                       >  1:28406/1‑139 (MQ=255)                                                                                                 accaaccaGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGtt                                   >  2:238843/1‑139 (MQ=255)                                                                                                 accaaccaGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGtt                                   <  1:508660/139‑1 (MQ=255)                                                                                                     accaGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAgg                                                          <  2:265736/112‑1 (MQ=255)                                                                                                     accaGGGTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAgg                                                          >  1:265736/1‑112 (MQ=255)                                                                                                         gggTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCaa                           <  1:168973/139‑1 (MQ=255)                                                                                                           gTTCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATg                         <  2:382075/139‑1 (MQ=255)                                                                                                            ttCCTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATgg                        >  2:305802/1‑139 (MQ=255)                                                                                                              ccTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAc                                                                        <  1:533718/89‑1 (MQ=255)                                                                                                              ccTGCGGTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAAc                                                                        >  2:533718/1‑89 (MQ=255)                                                                                                                    gTGGATTGTAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGt                <  1:505227/139‑1 (MQ=255)                                                                                                                            tAGTTTTCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCgtcgtc        >  2:179275/1‑139 (MQ=255)                                                                                                                                 ttCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCACGa    <  1:490575/138‑1 (MQ=255)                                                                                                                                  tCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCACGaa   <  1:547393/138‑1 (MQ=255)                                                                                                                                  tCCACCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCACGAAt  >  2:433875/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                       ATCACGCTGTCTTTGTGCTCTTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTCATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCATCCCCATTTTCGGCTCCGTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCATTACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCACGAAT  >  NZ_CP009273/60207‑60474

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑