Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,484,137	T→A	V362I (GTT→ATA)	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	1,484,137	0	T	A	90.9%	21.9 / ‑4.9	11	V362I (GTT→ATA)	unknown	Type II/IV secretion system ATP hydrolase TadA/VirB11/CpaF, TadA subfamily
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base A (7/3);  total (8/3)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGAGAAGCATTCCAAATGTTACAAGCAATGAATACCGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATAGCCCTCGCGATGCAACATCTCGCTTGGAAAGTATGGTTATGATGTCGAATGCATCCCTACCGTTAGAGGCAATTCGCCGTAATATCTCTTCAGCAGTAAACATAATAGTGCAGGCGTCCCGTTTAAATGATGGTTCAAGAAAAATTATGAATATCACTGAGGTTATGGGAATGGAAAACGGTCAAATCGTTTTACAGGATATATTTTCCTATAAGGCAAGTAAATATCGTGATAAAGAGGGTAAAATTCTTGGTGAGTTTATTAATCACGGACTACTAAC  >  1/1483900‑1484253                                                                                                                                                                                                                                              |                                                                                                                     tggAGAAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGaaa                                                                                                         <  1:462289/251‑1 (MQ=255) tggAGAAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGaa                                                                                                          <  1:676093/250‑1 (MQ=255)     gaAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGaaaatgg                                                                                                     >  1:390491/1‑248 (MQ=255)           ttCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAAt                                                                                               >  1:145787/1‑251 (MQ=255)           ttCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAAt                                                                                               >  1:775030/1‑251 (MQ=255)                                aacactggTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAATTGTTTTACAAGATATTTTTTc                                                                          <  1:401941/245‑1 (MQ=255)                                           cGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAATTGTTTTACAAGATATTTTTTCTTATAAGGCaa                                                               >  1:105586/1‑251 (MQ=255)                                           cGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAATTGTTTTACAAGATATTTTTTCTTATAAGGCaa                                                               >  1:833597/1‑251 (MQ=255)                                               ggTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAGAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAATTGTTTTACAAGATATTTTTTCTTATAAGGCAAGTaa                                                           >  1:438528/1‑251 (MQ=255)                                               ggTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAATTGTTTTACAAGATATTTTTTCTTATAAGGCAAGTaa                                                           >  1:323313/1‑251 (MQ=255)                                                                                                             ggTTATGATGTCGAATGCATCCCTACCGTTGGAGGCAATTCGCCGTAATATTTCTTCAGCAGTAAACATAATAGTGCAGGCGTCCCGCTTAAACGATGGTTCAAGAAAAATTATGAATATCACTGAAGTTATGGGAATGGAAAACGGTCAAATCGTTTTGCAAGATATATTTTCCTATAAGGCAAGTAAATATCGTGATAAAGAGGGTAAAATTCTTGGCGAGTTTATTAATCACGGACTACTAAc  >  1:507049/1‑246 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                     TGGAGAAGCATTCCAAATGTTACAAGCAATGAATACCGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATAGCCCTCGCGATGCAACATCTCGCTTGGAAAGTATGGTTATGATGTCGAATGCATCCCTACCGTTAGAGGCAATTCGCCGTAATATCTCTTCAGCAGTAAACATAATAGTGCAGGCGTCCCGTTTAAATGATGGTTCAAGAAAAATTATGAATATCACTGAGGTTATGGGAATGGAAAACGGTCAAATCGTTTTACAGGATATATTTTCCTATAAGGCAAGTAAATATCGTGATAAAGAGGGTAAAATTCTTGGTGAGTTTATTAATCACGGACTACTAAC  >  1/1483900‑1484253

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑