Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,494,539	T→C	F222S (TTC→TCC)	nanX →	MFS transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,494,539	0	T	C	87.1%	71.2 / 4.5	31	F222S (TTC→TCC)	nanX	MFS transporter
Reads supporting (aligned to +/- strand):  ref base T (2/2);  new base C (13/14);  total (15/16)
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

GAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACA  >  NZ_CP009273/4494463‑4494624                                                                             |                                                                                      gAAGGTAAATATAAGGATAAATCAACATTTTTGTGTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTAtttt                                                                          >  2:422558/1‑90 (MQ=255)      tAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCt                                                                     >  2:190328/1‑90 (MQ=255)      tAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCt                                                                     >  1:753363/1‑90 (MQ=255)               ggATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGc                                                            <  1:91931/90‑1 (MQ=255)                   aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                        <  2:177251/90‑1 (MQ=255)                   aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                        >  1:372827/1‑90 (MQ=255)                     aTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTg                                                      <  2:740679/90‑1 (MQ=255)                       cAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGc                                                    <  2:653438/90‑1 (MQ=255)                              tttGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATaaa                                             >  1:359884/1‑90 (MQ=255)                               ttGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAAc                                            <  1:364820/90‑1 (MQ=255)                                   ctgtctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGac                                        >  2:215491/1‑90 (MQ=255)                                       ctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGactact                                    <  2:12084/90‑1 (MQ=255)                                        ttCAGAAAACCACATCTTTAAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTActt                                   <  2:410645/90‑1 (MQ=255)                                              aaaCCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACttccttcc                             <  1:830081/90‑1 (MQ=255)                                               aaCCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTtccttcct                            >  1:560713/1‑90 (MQ=255)                                               aaCCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTtccttcct                            >  1:686251/1‑90 (MQ=255)                                               aaCCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTtccttcct                            >  1:812421/1‑90 (MQ=255)                                                       cTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCa                    <  1:145577/90‑1 (MQ=255)                                                          tCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGAt                 >  2:327248/1‑90 (MQ=255)                                                             aTCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTA‑TTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg             <  1:112225/90‑1 (MQ=255)                                                              tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg             <  2:55507/90‑1 (MQ=255)                                                              tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg             <  2:626085/90‑1 (MQ=255)                                                              tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg             <  2:688835/90‑1 (MQ=255)                                                              tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg             <  2:791990/90‑1 (MQ=255)                                                                tctATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa           <  1:753524/90‑1 (MQ=255)                                                                 ctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAg          >  2:345939/1‑90 (MQ=255)                                                                 ctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAg          >  2:665087/1‑90 (MQ=255)                                                                  tATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGt         >  2:76146/1‑90 (MQ=255)                                                                       tCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa           >  1:663494/1‑83 (MQ=255)                                                                       tCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa           <  2:663494/83‑1 (MQ=255)                                                                         gTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACa  >  1:424162/1‑90 (MQ=255)                                                                             |                                                                                      GAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACA  >  NZ_CP009273/4494463‑4494624

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑