Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,484,080	A→C	I343I (ATA→ATC)	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	1,484,080	0	A	C	94.7%	45.9 / ‑3.6	19	I343I (ATA→ATC)	unknown	Type II/IV secretion system ATP hydrolase TadA/VirB11/CpaF, TadA subfamily
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base C (12/6);  total (13/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

CTGAGCGTATTATTGTGGGCGAATGCCGTGGTGGAGAAGCATTCCAAATGTTACAAGCAATGAATACCGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATAGCCCTCGCGATGCAACATCTCGCTTGGAAAGTATGGTTATGATGTCGAATGCATCCCTACCGTTAGAGGCAATTCGCCGTAATATCTCTTCAGCAGTAAACATAATAGTGCAGGCGTCCCGTTTAAATGATGGTTCAAGAAAAATTATGAATATCACTGAGGTTATGGGAATGGAAAACGGTCAAATCGTTTTACAGGATATATTTTCCTATAAGGCAAGTAAATATCGTGATAAAGAGGGTAAAATTCTTGGTGAGTTTATTAATCACGGACTACTAAC  >  1/1483869‑1484253                                                                                                                                                                                                                    |                                                                                                                                                                              cTGAGCGTATTATCGTAGGTGAATGCCGTGGTGGAGAAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAAtc                                                                                                                                        <  1:281034/251‑2 (MQ=255)  tGAGCGTATTATCGTAGGTGAATGCCGTGGTGGAGAAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAAtca                                                                                                                                       <  1:782966/251‑3 (MQ=255)           tatcgtaggtgAATGCCGTGGTGGAGAAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAatatta                                                                                                                              >  1:405504/11‑249 (MQ=255)            atcgtaggtgAATGCCGTGGTGGAGAAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAatattac                                                                                                                             <  1:563338/242‑4 (MQ=255)            atcgtaggtgAATGCCGTGGTGGAGAAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAatatta                                                                                                                              >  1:629222/10‑248 (MQ=255)            atcgtaggtgAATGCCGTGGTGGAGAAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAatatta                                                                                                                              >  1:418153/10‑248 (MQ=255)                                tggAGAAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGaaa                                                                                                         <  1:462289/251‑1 (MQ=255)                                tggAGAAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGaa                                                                                                          <  1:676093/250‑1 (MQ=255)                                    gaAGCATTCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGaaaatgg                                                                                                     >  1:390491/1‑248 (MQ=255)                                          ttCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAatattac                                                                                                                             >  1:846452/1‑218 (MQ=255)                                          ttCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAAt                                                                                               >  1:775030/1‑251 (MQ=255)                                          ttCCAGATGTTACAAGCGATGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAAt                                                                                               >  1:145787/1‑251 (MQ=255)                                                           gaTGAACACTGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGaaataatgggtatgga                                                                                                           >  1:737220/2‑207 (MQ=255)                                                               aacactggTCACGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAATTGTTTTACAAGATATTTTTTc                                                                          <  1:401941/245‑1 (MQ=255)                                                                          cGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAATTGTTTTACAAGATATTTTTTCTTATAAGGCaa                                                               >  1:833597/1‑251 (MQ=255)                                                                          cGATGGTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAATTGTTTTACAAGATATTTTTTCTTATAAGGCaa                                                               >  1:105586/1‑251 (MQ=255)                                                                              ggTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAGAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAATTGTTTTACAAGATATTTTTTCTTATAAGGCAAGTaa                                                           >  1:438528/1‑251 (MQ=255)                                                                              ggTTCTATGTCAACGTTGCACGCAAATACCCCTCGGGATGCAACATCTCGATTGGAGAGTATGGTTATGATGTCGAATGCGTCCCTACCGTTGGAAGCAATTCGCCGTAATATTGCATCTGCAGTAAATATCATCGTACAAGCCTCCCGTTTAAATGATGGAACAAGAAAAATCATGAATATTACTGAAATAATGGGTATGGAAAATGGGCAAATTGTTTTACAAGATATTTTTTCTTATAAGGCAAGTaa                                                           >  1:323313/1‑251 (MQ=255)                                                                                                                                            ggTTATGATGTCGAATGCATCCCTACCGTTGGAGGCAATTCGCCGTAATATTTCTTCAGCAGTAAACATAATAGTGCAGGCGTCCCGCTTAAACGATGGTTCAAGAAAAATTATGAATATCACTGAAGTTATGGGAATGGAAAACGGTCAAATCGTTTTGCAAGATATATTTTCCTATAAGGCAAGTAAATATCGTGATAAAGAGGGTAAAATTCTTGGCGAGTTTATTAATCACGGACTACTAAc  >  1:507049/1‑246 (MQ=255)                                                                                                                                                                                                                    |                                                                                                                                                                              CTGAGCGTATTATTGTGGGCGAATGCCGTGGTGGAGAAGCATTCCAAATGTTACAAGCAATGAATACCGGTCACGATGGTTCTATGTCAACGTTGCACGCAAATAGCCCTCGCGATGCAACATCTCGCTTGGAAAGTATGGTTATGATGTCGAATGCATCCCTACCGTTAGAGGCAATTCGCCGTAATATCTCTTCAGCAGTAAACATAATAGTGCAGGCGTCCCGTTTAAATGATGGTTCAAGAAAAATTATGAATATCACTGAGGTTATGGGAATGGAAAACGGTCAAATCGTTTTACAGGATATATTTTCCTATAAGGCAAGTAAATATCGTGATAAAGAGGGTAAAATTCTTGGTGAGTTTATTAATCACGGACTACTAAC  >  1/1483869‑1484253

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑