Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,484,302	2 bp→GT	coding (1251‑1252/1281 nt)	unknown →	Type II/IV secretion system ATP hydrolase TadA/VirB11/CpaF, TadA subfamily

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,484,302	0	A	G	100.0%	20.4 / NA	9	E417E (GAA→GAG)	unknown	Type II/IV secretion system ATP hydrolase TadA/VirB11/CpaF, TadA subfamily
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (6/3);  total (6/3)
*	1	1,484,303	0	C	T	100.0%	18.7 / NA	9	L418L (CTA→TTA)	unknown	Type II/IV secretion system ATP hydrolase TadA/VirB11/CpaF, TadA subfamily
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (6/3);  total (6/3)

GGTCAAATCGTTTTACAGGATATATTTTCCTATAAGGCAAGTAAATATCGTGATAAAGAGGGTAAAATTCTTGGTGAGTTTATTAATCACGGACTACTAACTCGTTCTGTTGTATTCCAAAATGCTCAAGTATTCAATCTGAGTGCTGAACTACAAAGTATCTTCGGAGAAGCTGAGTAATGAATTATTATTTGTATTATGCCGTCCTAACAATAGGTGGGCTGTTATTTATATATACCTTAAGTAGTTGGTTTTCCACTAAAAGAAAAATTAATGAGTATGATACCTCTGTAAGTAGAACAAC  >  1/1484153‑1484456                                                                                                                                                      ||                                                                                                                                                          gggcAAATTGTTTTACAAGATATTTTTTCTTATAAGGCAAGTAAGTACCGTGATAAAGATGGCAAAATTATTGGTGAATTTGTTAACCATGGTTTATTAACTCGCTCTGCTGTTTTCCAAAATGCTCAAGTATTTAATCTGAGTACTGAGTTACAAAGTATTTTCGGAGAAGCTGAGTGATGAGCCATTATTTATATTATGCCGTCCTTACAATAGGTGGACTATTATTTATATATACCTTAAGTAGTTgg                                                       >  1:322659/4‑251 (MQ=255)                                  aaGGCAAGTAAGTACCGTGATAAAGATGGCAAAATTATTGGTGAATTTGTTAACCATGGTTTATTAACTCGCTCTGCTGTTTTCCAAAATGCTCAAGTATTTAATCTGAGTACTGAGTTACAAAGTATTTTCGGAGAAGCTGAGTGATGAGCCATTATTTATATTATGCCGTCCTTACAATAGGTGGACTATTATTTATATATACCTTAAGTAGTTGGTTTTCTACTAAAAGAAAAATTAATGAGTATGAt                      <  1:604769/251‑1 (MQ=255)                                   aGGCAAGTAAGTACCGTGATAAAGATGGCAAAATTATTGGTGAATTTGTTAACCATGGTTTATTAACTTGCTCTGCTGTTTTCCAAAATGCTCAAGTATTTAATCTGAGTACTGAGTTACAAAGTATTTTCGGAGAAGCTGAGTGATGAGCCATTATTTATATTATGCCGTCCTTACAATAGGTGGACTATTATTTATATATACCTTAAGTAGTTGGTTTTCTACTAAAAGAAAAATTAATGAGTATGATa                     >  1:699117/1‑251 (MQ=255)                                     gCAAGTAAGTACCGTGATAAAGATGGCAAAATTATTGGTGAATTTGTTAACCATGGTTTATTAACTCGCTCTGCTGTTTTCCAAAATGCTCAAGTATTTAATCTGAGTACTGAGTTACAAAGTATTTTCGGAGAAGCTGAGTGATGAGCCATTATTTATATTATGCCGTCCTTACAATAGGTGGACTATTATTTATATATACCTTAAGTAGTTGGTTTTCTACTAAAAGAAAAATTAATGAGTATGATAc                    >  1:818760/1‑250 (MQ=255)                                        agtaagtaCCGTGATAAAGATGGCAAAATTATTGGTGAATTTGTTAACCATGGTTTATTAACTCGCTCTGCTGTTTTCCAAAATGCTCAAGTATTTAATCTGAGTACTGAGTTACAAAGTATTTTCGGAGAAGCTGAGTGATGAGCCATTATTTATATTATGCCGTCCTTACAATAGGTGGACTATTATTTATATATACCTTAAGTAGTTGGTTTTCTACTAAAAGAAAAATTAATg                              >  1:549885/1‑237 (MQ=255)                                                 cGTGATAAAGATGGCAAAATTATTGGTGAATTTGTTAACCATGGTTTATTAACTCGCTCTGCTGTTTTCCAAAATGCTCAAGTATTTAATCTGAGTACTGAGTTACAAAGTATTTTCGGAGAAGCTGAGTGATGAGCCATTATTTATATTATGCCGTCCTTACAATAGGTGGACTATTATTTATATATACCTTAAGTAGTTGGTTTTCTACTAAAAGAAAAATTAATGAGTATGAt                      >  1:794038/1‑236 (MQ=255)                                                      tAAAGATGGCAAAATTATTGGTGAATTTGTTAACCATGGTTTATTAACTCGCTCTGCTGTTTTCCAAAATGCTCAAGTATTTAATCTGAGTACTGAGTTACAAAGTATTTTCGGAGAAGCTGAGTGATGAGCCATTATTTATATTATGCCGTCCTTACAATAGGTGGACTATTATTTATATATACCTTAAGTAGTTGGTTTTCTACTAAAAGAAAAATTAATGAGTATGATACCTCTATAAGTAGgacaac  <  1:538473/251‑1 (MQ=255)                                                                                                             gctgtttttcAAAATGCTCAAGTATTTAATCTGAGTACTGAGTTACAAAGTATTTTCGGAGAAGCTGAGTGATGAGCCATTATTTATATTATGCCGTCCTTACAATAGGTGGACTATTATTTATATATACCTTAAGTAGTTGGTTTTCTACTAAAAGAAAAATTAATGAGTATGATAc                    <  1:441381/169‑1 (MQ=255)                                                                                                                                          tCTGAGTACTGAGTTACAAAGTATTTTCGGAGAAGCTGAGTGATGAGCCATTATTTATATTATGCCGTCCTTACAATAGGTGGACTATTATTTATATATACCTTAAGTAGTTGGTTTTCTACTAAAAGAAAAATTAATGAGTATGATACCTCTATAAGTAggac     >  1:274068/1‑161 (MQ=255)                                                                                                                                                      ||                                                                                                                                                          GGTCAAATCGTTTTACAGGATATATTTTCCTATAAGGCAAGTAAATATCGTGATAAAGAGGGTAAAATTCTTGGTGAGTTTATTAATCACGGACTACTAACTCGTTCTGTTGTATTCCAAAATGCTCAAGTATTCAATCTGAGTGCTGAACTACAAAGTATCTTCGGAGAAGCTGAGTAATGAATTATTATTTGTATTATGCCGTCCTAACAATAGGTGGGCTGTTATTTATATATACCTTAAGTAGTTGGTTTTCCACTAAAAGAAAAATTAATGAGTATGATACCTCTGTAAGTAGAACAAC  >  1/1484153‑1484456

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑