Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,536,840	A→G	E643G (GAA→GGA)	fimD →	fimbrial usher FimD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,536,840	0	A	G	100.0%	88.4 / NA	25	E643G (GAA→GGA)	fimD	fimbrial usher FimD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (12/13);  total (12/13)

GGCGACATGCCAGTGCCAGCTACAGCATGTCACACGATCTCAACGGTCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGAAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACGCCACGC  >  NZ_CP009273/4536753‑4536923                                                                                        |                                                                                    ggCGACATGCCAGTGCCAGCTACAGCATGTCACACGATCTCAACGGTCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGGAg                                                                                   <  2:374999/90‑1 (MQ=255)   cGACATGCCAGTGCCAGCTACAGCATGTCACACGATCTCAACGGTCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGGAGac                                                                                 >  1:255659/1‑90 (MQ=255)          ccagtgccagCTACAGCATGTCACACGATCTCAATGGTCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGGAGACAACAAcc                                                                          <  2:337255/90‑1 (MQ=255)          ccagtgccagCTACAGCATGTCACACGATCTCAACGGTCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGGAGACAACAAcc                                                                          <  2:46205/90‑1 (MQ=255)          ccagtgccagCTACAGCATGTCACACGATCTCAACGGTCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGGAGACAACAAcc                                                                          <  1:339100/90‑1 (MQ=255)                         gCATGTCACACGATCTCAACGGTCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGc                                                           >  1:345891/1‑90 (MQ=255)                             gTCACACGATCTCAACGGTCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAAc                                                       <  1:128137/90‑1 (MQ=255)                                 cacGATCTCAACGGTCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGc                                                   >  1:246848/1‑90 (MQ=255)                                  acGATCTCAACGGTCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCt                                                  <  1:40661/90‑1 (MQ=255)                                              gTCGGATGACCAATCTGGCTGGTGTATACGGGACGTTGCTGGGAGACAACAACCGCAGCTGTAGCGTGGAAACCGGCTATGCGGGGGGAg                                      >  2:248121/1‑90 (MQ=255)                                               tCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAgg                                     >  2:167666/1‑90 (MQ=255)                                                  gATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGa                                  <  1:286587/90‑1 (MQ=255)                                                       ccAATCTGGCTGGTGTATACGGTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGaa                             >  2:287477/1‑90 (MQ=255)                                                                    tgtATACGGTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTAc                <  1:167666/90‑1 (MQ=255)                                                                        taCGGTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGc            >  1:222128/1‑90 (MQ=255)                                                                            gTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACg        >  2:370128/1‑90 (MQ=255)                                                                            gTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACg        >  1:437052/1‑90 (MQ=255)                                                                            gTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACg        >  1:122734/1‑90 (MQ=255)                                                                            gTACGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACg        >  1:148398/1‑90 (MQ=255)                                                                              aCGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACGcc      <  2:119680/90‑1 (MQ=255)                                                                              aCGTTGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACGcc      <  1:274517/90‑1 (MQ=255)                                                                                 ttGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACGCCACg   >  2:30045/1‑90 (MQ=255)                                                                                  tGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACGCCACGc  <  1:46092/90‑1 (MQ=255)                                                                                  tGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACGCCACGc  <  2:359904/90‑1 (MQ=255)                                                                                  tGCTGGGAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACGCCACGc  <  2:517781/90‑1 (MQ=255)                                                                                        |                                                                                    GGCGACATGCCAGTGCCAGCTACAGCATGTCACACGATCTCAACGGTCGGATGACCAATCTGGCTGGTGTATACGGTACGTTGCTGGAAGACAACAACCTCAGCTATAGCGTGCAAACCGGCTATGCCGGGGGAGGCGATGGAAATAGCGGAAGTACAGGCTACGCCACGC  >  NZ_CP009273/4536753‑4536923

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: ‑