Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	465,464	T→C	S380P (TCG→CCG)	mdlA →	SmdA family multidrug ABC transporter permease/ATP‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	465,464	0	T	C	100.0%	114.9 / NA	36	S380P (TCG→CCG)	mdlA	SmdA family multidrug ABC transporter permease/ATP‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (19/17);  total (19/17)

CGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTG  >  NZ_CP009273/465378‑465549                                                                                       |                                                                                      cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc                                                                                    >  2:32123/1‑90 (MQ=255) cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc                                                                                    <  2:1357404/90‑1 (MQ=255) cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc                                                                                    <  2:1238220/90‑1 (MQ=255)     ggAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCAt                                                                                >  2:736175/1‑90 (MQ=255)     ggAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCAt                                                                                >  2:1452788/1‑90 (MQ=255)          aCGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc                                                                                    >  2:1201933/1‑81 (MQ=255)          aCGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc                                                                                    <  1:1201933/81‑1 (MQ=255)          aCGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGc                                                                           >  1:574139/1‑90 (MQ=255)            gTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGt                                                                         <  2:834459/90‑1 (MQ=255)            gTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGt                                                                         <  2:742577/90‑1 (MQ=255)            gTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGt                                                                         <  1:43926/90‑1 (MQ=255)                     gCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGAc                                                                >  1:251400/1‑90 (MQ=255)                        cTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTc                                                             <  2:975049/90‑1 (MQ=255)                             aCCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCTGCGTCATTTCGACGTCAGCGa                                                        <  1:782941/90‑1 (MQ=255)                               ccGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAgg                                                      <  2:916791/90‑1 (MQ=255)                               ccGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAgg                                                      <  2:1184548/90‑1 (MQ=255)                                cGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAggg                                                     <  1:1092296/90‑1 (MQ=255)                                      gATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGatat                                               >  2:189614/1‑90 (MQ=255)                                        tGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTc                                             <  2:22372/90‑1 (MQ=255)                                            gggTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCtt                                         >  1:312667/1‑90 (MQ=255)                                             gttATCTGCGGGCCGACTGTTTCCGGCAAAAGTAACCTTTTGCCGCTCATTCAGCGTCATTTCCCCGTCAGCGAGGGGGATATTCGCttt                                        <  1:1082761/88‑1 (MQ=255)                                              gTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTc                                       >  1:981256/1‑90 (MQ=255)                                              gTATCTGCGGGCCGACTGGTTCCGGCAAAAGAACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTc                                       >  1:858890/1‑90 (MQ=255)                                                aTCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAt                                     >  1:818338/1‑90 (MQ=255)                                                aTCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAt                                     <  1:1146291/90‑1 (MQ=255)                                                    gCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGata                                 <  1:1279236/90‑1 (MQ=255)                                                     cGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGatat                                <  1:607172/90‑1 (MQ=255)                                                      gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATAtt                               >  2:483422/1‑90 (MQ=255)                                                      gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATAtt                               >  1:1199333/1‑90 (MQ=255)                                                      gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATAtt                               >  1:1103123/1‑90 (MQ=255)                                                      gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATAtt                               >  1:636647/1‑90 (MQ=255)                                                        gCCGACTGGTTCCGGCGAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTcc                             >  2:123848/1‑90 (MQ=255)                                                           gACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCctct                          >  1:502237/1‑90 (MQ=255)                                                               ggTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACg                      <  2:1560320/90‑1 (MQ=255)                                                                         aaaGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAAc            >  1:1549712/1‑90 (MQ=255)                                                                               cccTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATa      >  2:531882/1‑90 (MQ=255)                                                                                   gttgcCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTg  >  1:375911/1‑90 (MQ=255)                                                                                   gttgcCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTg  >  1:594155/1‑90 (MQ=255)                                                                                   gttgcCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTg  >  2:324386/1‑90 (MQ=255)                                                                                   gttgcCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTg  >  1:82826/1‑90 (MQ=255)                                                                                       |                                                                                      CGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTG  >  NZ_CP009273/465378‑465549

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑