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%	77.1 / NA	23	F44S (TTC→TCC)	rpmE	50S ribosomal protein L31
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (10/13);  total (10/13)

CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAA  >  NZ_CP009273/4116985‑4117150                                                                                       |                                                                                ctgctCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCAc                                                                              <  2:555166/90‑1 (MQ=255)        tGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCaaa                                                                       >  1:1593/1‑90 (MQ=255)        tGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCaaa                                                                       <  1:360976/90‑1 (MQ=255)         gCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAAc                                                                      <  2:733723/90‑1 (MQ=255)         gCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTACCACCCGTTCTCCACTGGCAAAc                                                                      <  1:161077/90‑1 (MQ=255)               aCGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTg                                                                <  1:608549/90‑1 (MQ=255)                cGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGa                                                               <  1:524664/90‑1 (MQ=255)                  tAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATg                                                             <  2:411036/90‑1 (MQ=255)                    aTGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGtt                                                           >  2:593677/1‑90 (MQ=255)                      gAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGc                                                         <  2:208053/90‑1 (MQ=255)                                         ggTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGAc                                      <  1:567896/90‑1 (MQ=255)                                              tGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCtt                                 >  1:244636/1‑90 (MQ=255)                                                    gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa                           >  1:75809/1‑90 (MQ=255)                                                    gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa                           >  2:412564/1‑90 (MQ=255)                                                        cTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGt                       <  1:412564/90‑1 (MQ=255)                                                         tCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGtt                      >  2:498543/1‑90 (MQ=255)                                                                       aaGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGATGCTACCGGTGGCCGTGTTGACCGCTTCAACGAGCGGTTCAACATCCCGGgc        >  1:269287/1‑90 (MQ=255)                                                                         gTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcag      <  1:722927/90‑1 (MQ=255)                                                                         gTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcag      <  2:12452/90‑1 (MQ=255)                                                                          tGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcagc     >  2:375897/1‑90 (MQ=255)                                                                             cACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcagc     >  1:721546/1‑87 (MQ=255)                                                                             cACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcagc     <  2:721546/87‑1 (MQ=255)                                                                             cACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCaaa  >  1:753232/1‑90 (MQ=255)                                                                                       |                                                                                CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAA  >  NZ_CP009273/4116985‑4117150

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑