Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,102,646	T→C	G140G (GGA→GGG)	wzx ←	O16 family O‑antigen flippase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,102,646	0	T	C	100.0%	98.3 / NA	29	G140G (GGA→GGG)	wzx	O16 family O‑antigen flippase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (13/16);  total (13/16)

TTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTA  >  NZ_CP009273/2102560‑2102727                                                                                       |                                                                                  tttGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTcccc                                                                                <  2:472728/90‑1 (MQ=255)       ttCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAAc                                                                          <  1:74427/90‑1 (MQ=255)        tCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACa                                                                         >  1:865715/1‑90 (MQ=255)          acaAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGc                                                                       <  1:1162078/90‑1 (MQ=255)          acaAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGc                                                                       <  1:918623/90‑1 (MQ=255)           caAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGcc                                                                      <  2:201648/90‑1 (MQ=255)               aataaatGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGAt                                                                  <  1:1113762/90‑1 (MQ=255)               aataaatGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGAt                                                                  <  1:696543/90‑1 (MQ=255)                        tAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGAt                                                         >  1:1202930/1‑90 (MQ=255)                              gATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAAtt                                                   >  1:1157393/1‑90 (MQ=255)                              gATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAAtt                                                   >  2:743903/1‑90 (MQ=255)                                     gCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACt                                            >  2:483889/1‑90 (MQ=255)                                         aGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATg                                        >  2:214126/1‑90 (MQ=255)                                                     tactacTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACg                            <  2:212199/90‑1 (MQ=255)                                                       ctactTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCa                                      >  1:981740/1‑78 (MQ=255)                                                       ctactTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCa                                      <  2:981740/78‑1 (MQ=255)                                                       ctactTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGAc                          >  1:798169/1‑90 (MQ=255)                                                        tactTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGAcc                         <  1:743903/90‑1 (MQ=255)                                                            tAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCatat                     >  2:1142680/1‑90 (MQ=255)                                                            tAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCatat                     >  1:614632/1‑90 (MQ=255)                                                            tAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCatat                     >  1:477306/1‑90 (MQ=255)                                                            tAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCatat                     <  1:249967/90‑1 (MQ=255)                                                                   aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACg                            >  1:996410/1‑76 (MQ=255)                                                                   aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACg                            <  2:996410/76‑1 (MQ=255)                                                                   aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACg              >  2:417234/1‑90 (MQ=255)                                                                      catttcatttTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCa           <  2:97949/90‑1 (MQ=255)                                                                        tttcatttTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATg         <  2:51215/90‑1 (MQ=255)                                                                          tcatttTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCt       <  2:992497/90‑1 (MQ=255)                                                                             ttttttCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGt    <  1:1099276/90‑1 (MQ=255)                                                                             ttttttCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGt    <  2:200113/90‑1 (MQ=255)                                                                               ttttctttccCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTta  <  1:173111/90‑1 (MQ=255)                                                                               ttttctttccCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTta  <  1:1174354/90‑1 (MQ=255)                                                                                       |                                                                                  TTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTA  >  NZ_CP009273/2102560‑2102727

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑