Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,484,242	C→T	H397H (CAC→CAT)	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	1,484,242	0	C	T	87.5%	10.6 / ‑4.0	8	H397H (CAC→CAT)	unknown	Type II/IV secretion system ATP hydrolase TadA/VirB11/CpaF, TadA subfamily
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (5/2);  total (6/2)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

GGTTATGATGTCGAATGCATCCCTACCGTTAGAGGCAATTCGCCGTAATATCTCTTCAGCAGTAAACATAATAGTGCAGGCGTCCCGTTTAAATGATGGTTCAAGAAAAATTATGAATATCACTGAGGTTATGGGAATGGAAAACGGTCAAATCGTTTTACAGGATATATTTTCCTATAAGGCAAGTAAATATCGTGATAAAGAGGGTAAAATTCTTGGTGAGTTTATTAATCACGGACTACTAACTCGTTCTGTTGTATTCCAAAATGCTCAAGTATTCAATCTGAGTGCTGAACTACAAAGTATCTTCGGAGAAGCTGAGTAATGAATTATTATTTGTATTATGCCGTCCTAACAATAGGTGGGCTGTTATTTATATATACCTTAAGTAGTTGGTTTTCCACTAAAAGAAAAATTAATGAGTATGATACCTCTGTAAGTAGAACAAC  >  1/1484008‑1484456                                                                                                                                                                                                                                           |                                                                                                                                                                                                                       ggTTATGATGTCGAATGCATCCCTACCGTTGGAGGCAATTCGCCGTAATATTTCTTCAGCAGTAAACATAATAGTGCAGGCGTCCCGCTTAAACGATGGTTCAAGAAAAATTATGAATATCACTGAAGTTATGGGAATGGAAAACGGTCAAATCGTTTTGCAAGATATATTTTCCTATAAGGCAAGTAAATATCGTGATAAAGAGGGTAAAATTCTTGGCGAGTTTATTAATCACGGACTACTAAc                                                                                                                                                                                                             >  1:507049/1‑246 (MQ=255)                                                                                                                                                  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)                                                                                                                                                                                                                                           |                                                                                                                                                                                                                       GGTTATGATGTCGAATGCATCCCTACCGTTAGAGGCAATTCGCCGTAATATCTCTTCAGCAGTAAACATAATAGTGCAGGCGTCCCGTTTAAATGATGGTTCAAGAAAAATTATGAATATCACTGAGGTTATGGGAATGGAAAACGGTCAAATCGTTTTACAGGATATATTTTCCTATAAGGCAAGTAAATATCGTGATAAAGAGGGTAAAATTCTTGGTGAGTTTATTAATCACGGACTACTAACTCGTTCTGTTGTATTCCAAAATGCTCAAGTATTCAATCTGAGTGCTGAACTACAAAGTATCTTCGGAGAAGCTGAGTAATGAATTATTATTTGTATTATGCCGTCCTAACAATAGGTGGGCTGTTATTTATATATACCTTAAGTAGTTGGTTTTCCACTAAAAGAAAAATTAATGAGTATGATACCTCTGTAAGTAGAACAAC  >  1/1484008‑1484456

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑