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	91.1%	127.0 / 5.1	45	F222S (TTC→TCC)	nanX	MFS transporter
Reads supporting (aligned to +/- strand):  ref base T (2/2);  new base C (18/23);  total (20/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.76e-01

GATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAG  >  NZ_CP009273/4494466‑4494625                                                                          |                                                                                       gATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGt                                                                        >  1:702989/1‑90 (MQ=255)   tAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCt                                                                      >  1:384022/1‑90 (MQ=255)    aaaTATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTa                                                                     >  2:997239/1‑90 (MQ=255)      atatAAGGATAAATCAACATTTTTGTCTGTCTTCATAAAGCCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTAtt                                                                   <  1:135501/90‑1 (MQ=255)              aTAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCaa                                                           >  2:297315/1‑90 (MQ=255)                aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                         >  1:126323/1‑90 (MQ=255)                aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                         >  1:386545/1‑90 (MQ=255)                aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                         >  2:384410/1‑90 (MQ=255)                aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                         >  1:529609/1‑90 (MQ=255)                aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc                                                         >  2:522551/1‑90 (MQ=255)                      aCATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCg                                                   >  1:730809/1‑90 (MQ=255)                      aCATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCg                                                   >  2:622630/1‑90 (MQ=255)                       cATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGa                                                  <  2:730809/90‑1 (MQ=255)                         tttttGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGaaa                                                <  2:193796/90‑3 (MQ=255)                            ttGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAAc                                             <  1:913832/90‑1 (MQ=255)                            ttGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAAc                                             <  2:895046/90‑1 (MQ=255)                             tgtctgtcTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACg                                            <  2:131537/90‑1 (MQ=255)                              gtctgtctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACgg                                           >  2:29234/1‑90 (MQ=255)                                ctgtctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGac                                         <  1:794370/90‑1 (MQ=255)                                ctgtctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGac                                         <  1:483452/90‑1 (MQ=255)                                ctgtctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGac                                         <  1:379437/90‑1 (MQ=255)                                 tgtctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGact                                        <  2:773001/90‑1 (MQ=255)                                    ctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGactact                                     <  2:214933/90‑1 (MQ=255)                                    ctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGactact                                     <  2:11602/90‑1 (MQ=255)                                    ctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGactact                                     <  1:268092/90‑1 (MQ=255)                                              ccACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTAc                           >  2:690065/1‑90 (MQ=255)                                                tcaTCTTTCAATCTCTATGATCGTTGCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCt                         <  1:646163/89‑1 (MQ=255)                                                  aTCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTgg                       <  2:126323/90‑1 (MQ=255)                                                   tCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGc                      >  2:86201/1‑90 (MQ=255)                                                    cTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCa                     <  1:29234/90‑1 (MQ=255)                                                    cTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCa                     <  1:473984/90‑1 (MQ=255)                                                           tctcTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg              <  2:386545/90‑1 (MQ=255)                                                           tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATa                                                <  1:302851/56‑1 (MQ=255)                                                           tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATa                                                >  2:302851/1‑56 (MQ=255)                                                           tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg              <  1:800750/90‑1 (MQ=255)                                                           tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg              <  2:66463/90‑1 (MQ=255)                                                             tctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa            <  1:108636/90‑1 (MQ=255)                                                             tctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa            <  2:389716/90‑1 (MQ=255)                                                             tctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa            >  1:925535/1‑90 (MQ=255)                                                             tctATGATCGTTTCCCACGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa            >  2:387708/1‑90 (MQ=255)                                                              ctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGTAg           >  2:126000/1‑90 (MQ=255)                                                               tATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGt          >  1:10824/1‑90 (MQ=255)                                                                aTGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGtt         <  1:321119/90‑1 (MQ=255)                                                                aTGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGtt         <  2:10824/90‑1 (MQ=255)                                                                      gTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACa   >  2:931434/1‑90 (MQ=255)                                                                       tttcCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAg  <  1:86201/90‑1 (MQ=255)                                                                          |                                                                                       GATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAG  >  NZ_CP009273/4494466‑4494625

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑