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%	131.7 / NA	38	F44S (TTC→TCC)	rpmE	50S ribosomal protein L31
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (21/17);  total (21/17)

CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATA  >  NZ_CP009273/4116985‑4117152                                                                                       |                                                                                  ctgctCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCAc                                                                                <  1:100332/90‑1 (MQ=255)    ctctTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGATCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTgg                                                                             <  1:837747/90‑1 (MQ=255)       ttGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCaa                                                                          <  1:143193/90‑1 (MQ=255)       ttGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCaa                                                                          <  2:112939/90‑1 (MQ=255)         gCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAAc                                                                        <  1:163444/90‑1 (MQ=255)              aaCGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGt                                                                   >  2:853218/1‑90 (MQ=255)              aaCGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGt                                                                   >  1:839915/1‑90 (MQ=255)              aaCGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGt                                                                   >  1:592826/1‑90 (MQ=255)                cGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGa                                                                 <  1:691140/90‑1 (MQ=255)                  tAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATg                                                               <  2:278746/90‑1 (MQ=255)                   aaTGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGt                                                              >  1:656805/1‑90 (MQ=255)                   aaTGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGt                                                              >  2:47460/1‑90 (MQ=255)                          aTCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTAcc                                                       >  2:442649/1‑90 (MQ=255)                            ccGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAAc                                                                        <  2:234283/71‑1 (MQ=255)                            ccGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAAc                                                                        >  1:234283/1‑71 (MQ=255)                              gCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTg                                                   >  1:407417/1‑90 (MQ=255)                              gCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTg                                                   >  2:666714/1‑90 (MQ=255)                               cTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTgg                                                  <  2:594420/90‑1 (MQ=255)                                  cACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCg                                               <  2:781785/90‑1 (MQ=255)                                         ggTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGAc                                        >  1:709043/1‑90 (MQ=255)                                         ggTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGAc                                        >  1:660179/1‑90 (MQ=255)                                           tCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCg                                      >  1:469434/1‑90 (MQ=255)                                             aTGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCt                                    <  1:603991/90‑1 (MQ=255)                                               gACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTc                                  <  1:988636/90‑1 (MQ=255)                                                    gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa                             >  2:613525/1‑90 (MQ=255)                                                    gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTcaacaa                             <  1:997214/90‑1 (MQ=255)                                                    gAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGGGTTGACCGCTTcaacaa                             >  1:20462/1‑90 (MQ=255)                                                         tCGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGtt                        >  1:588882/1‑90 (MQ=255)                                                          cGACGTGTGCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGttt                       >  1:660574/1‑90 (MQ=255)                                                               tgtgCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACa                  <  1:33542/90‑1 (MQ=255)                                                                gtgCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTgg                                                  <  2:468598/57‑1 (MQ=255)                                                                gtgCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTgg                                                  >  1:468598/1‑57 (MQ=255)                                                                gtgCAGCAAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACAt                 >  2:112608/1‑90 (MQ=255)                                                                     gcaAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCgg            <  2:588882/90‑1 (MQ=255)                                                                     gcaAGTGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCgg            <  2:660179/90‑1 (MQ=255)                                                                          tGCCACCCGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGgcagc       >  2:374432/1‑90 (MQ=255)                                                                               cccGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATa  >  2:334735/1‑90 (MQ=255)                                                                               cccGTTCTCCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATa  >  1:876888/1‑90 (MQ=255)                                                                                       |                                                                                  CTGCTCTTGCGGTAACGTAATGAAAATCCGCTCCACCGTTGGTCATGACCTGAACCTCGACGTGTGCAGCAAGTGCCACCCGTTCTTCACTGGCAAACAGCGTGATGTTGCTACCGGTGGCCGTGTTGACCGCTTCAACAAGCGTTTCAACATCCCGGGCAGCAAATA  >  NZ_CP009273/4116985‑4117152

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑