Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,117,071	T→C	F44S (TTC→TCC)	rpmE →	50S ribosomal protein L31

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,117,071	0	T	C	100.0%	69.1 / NA	22	F44S (TTC→TCC)	rpmE	50S ribosomal protein L31
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (13/9);  total (13/9)

CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGAC  >  NZ_CP009273/4116985‑4117156                                                                                       |                                                                                      ctgctCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCAc                                                                                    <  2:234258/90‑1 (MQ=255) ctgctCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCAc                                                                                    >  1:102434/1‑90 (MQ=255)       ttGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCaa                                                                              <  2:12619/90‑1 (MQ=255)        tGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCaaa                                                                             <  2:264009/90‑1 (MQ=255)                    aTGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGtt                                                                 >  2:615444/1‑90 (MQ=255)                          aTCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTAcc                                                           >  1:57653/1‑90 (MQ=255)                             cGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGt                                                        <  1:140288/90‑1 (MQ=255)                                         ggTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGAc                                            >  1:283442/1‑90 (MQ=255)                                              tGACCTGAACCTGGGCGCGGGCGGCAAGTGCCACCCGTTCTCCACTTTAAAACAGCGCGATGTTGCGACCGGTGGGCGTGTTGACCGCtt                                       >  1:120122/1‑90 (MQ=255)                                                    gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa                                 <  1:456982/90‑1 (MQ=255)                                                         tCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGtt                            >  1:306714/1‑90 (MQ=255)                                                          cGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATg                                                                   <  1:60067/50‑1 (MQ=255)                                                          cGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATg                                                                   >  2:60067/1‑50 (MQ=255)                                                          cGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGttt                           >  2:380948/1‑90 (MQ=255)                                                          cGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGttt                           >  2:498736/1‑90 (MQ=255)                                                                gtgCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGAc                                            <  1:694638/67‑1 (MQ=255)                                                                gtgCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGAc                                            >  2:694638/1‑67 (MQ=255)                                                                gtgCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACAt                     >  1:192816/1‑90 (MQ=255)                                                                      caAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa                                 >  1:62456/1‑72 (MQ=255)                                                                      caAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa                                 <  2:62456/72‑1 (MQ=255)                                                                         gTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcag            <  1:431924/90‑1 (MQ=255)                                                                               cccGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATa      >  1:143711/1‑90 (MQ=255)                                                                                   ttctccACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGAc  >  1:290684/1‑90 (MQ=255)                                                                                       |                                                                                      CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATAAGAC  >  NZ_CP009273/4116985‑4117156

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑