Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,544,363	+C	coding (169/1314 nt)	gntT →	gluconate permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,544,363	1	.	C	98.1%	128.3 / ‑5.3	53	V57L (GTC→CTC)	gntT	gluconate permease
Reads supporting (aligned to +/- strand):  ref base . (0/0);  major base C (29/23);  minor base A (1/0);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01

GATTAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTC‑G‑‑C‑GGACG‑TCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCAAAATGCTGGCAG  >  NC_000913/3544301‑3544420                                                                    |                                                          gATTAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCt                                                 >  1:4582044/1‑76 (MQ=255)  agtAATGCAAGGAAGGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCtt                                                <  2:121389/74‑1 (MQ=255)  aTTAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCtt                                                <  2:3160849/76‑1 (MQ=255)  aTTAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCtt                                                <  1:4494688/76‑1 (MQ=255)   ttAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGGCGCTCGGTAGCCTTg                                               >  2:3893634/1‑76 (MQ=255)     aaTGCAAGGAATGCCGCTGGATAAAGGTATTGGCTCCATCAAAGACGGTGGCGG‑‑CGGGACGCTCGGTAGCCGTGcc                                             >  2:3133371/1‑76 (MQ=255)      aTGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCCTGccc                                            >  1:2385720/1‑76 (MQ=255)       tGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCt                                           <  2:1996063/76‑1 (MQ=255)         gaaGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGa                                         <  2:4677860/75‑1 (MQ=255)         cAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGa                                         >  1:4418714/1‑76 (MQ=255)          aaGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGAt                                        >  2:3802606/1‑76 (MQ=255)           aGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATc                                       <  1:2135028/76‑1 (MQ=255)             gAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCAt                                     <  1:1422462/76‑1 (MQ=255)              aaTGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATg                                    <  2:3498004/76‑1 (MQ=255)                tGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATggg                                  <  1:2263696/76‑1 (MQ=255)                 gCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGt                                 >  1:3543629/1‑76 (MQ=255)                 gCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGt                                 <  1:1713805/76‑1 (MQ=255)                 gCCGCGGGATAAAGTGATTGGCTCCAGCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGt                                 <  1:1744085/76‑1 (MQ=255)                   cGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGttt                               >  1:4371740/1‑76 (MQ=255)                    gCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGtttt                              <  2:1206368/76‑1 (MQ=255)                       ggATAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGgc                           <  1:1466012/76‑1 (MQ=255)                          tAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCa                        >  1:1719148/1‑76 (MQ=255)                          tAAAGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTCGCGCa                        >  2:2948801/1‑76 (MQ=255)                           aaaGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCaa                       >  1:1811736/1‑76 (MQ=255)                           aaaGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCaa                       <  1:2204388/76‑1 (MQ=255)                           aaaGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCaa                       <  1:2223213/76‑1 (MQ=255)                           aaaGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCaa                       <  2:3022570/76‑1 (MQ=255)                           aaaGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGATCGGTAGCCTTGCCCTGATCATGGGGTTTGGCGCaa                       >  1:3122916/1‑76 (MQ=255)                            aaGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAAt                      <  2:4705212/76‑1 (MQ=255)                             aGTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATg                     >  2:1471634/1‑76 (MQ=255)                              gTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATggg                                  <  2:689754/62‑1 (MQ=255)                              gTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATggg                                  >  1:689754/1‑62 (MQ=255)                              gTTATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGACCATGGGGTTTGGCGCACTGc                    >  2:4697409/1‑76 (MQ=255)                               ttATTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCt                   <  2:4240185/76‑1 (MQ=255)                                 aTTGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTgg                 >  1:3908963/1‑76 (MQ=255)                                 aTTAGCTCCATCACAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATTCTgg                 <  1:3976689/76‑1 (MQ=255)                                  tgggCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTggg                <  2:4059328/74‑1 (MQ=255)                                   tGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGc               >  2:4414442/1‑76 (MQ=255)                                   tGGCTCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGc               >  1:4603773/1‑76 (MQ=255)                                   tGGCTCCATCAAAGCCGGTGTC‑GGAG‑GGACGCTCGGCAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGc               >  2:2554089/1‑76 (MQ=255)                                     ggtCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCaa             <  2:4402716/74‑1 (MQ=255)                                       tCCATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCaaaa           >  2:1569319/1‑76 (MQ=255)                                        ccATCAAAGCCGGTGTCGG‑‑CTGGACGCTCGGTCGCCCTGCCCCGATCCTGGGTTTTGGCGTAATGCTGCGCaaact          >  2:534431/1‑74 (MQ=255)                                        ccATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCAAAAt          >  2:1224392/1‑76 (MQ=255)                                        ccATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCAAAAt          >  2:2761323/1‑76 (MQ=255)                                        ccATCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCAAAAt          >  1:1110938/1‑76 (MQ=255)                                         caacAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCAAAATg         <  2:4783820/73‑1 (MQ=255)                                          aTCAAAGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCAAAATGc        >  1:605890/1‑76 (MQ=255)                                           tCAAAGCCGGTGTCGG‑‑CGGGACGCCCGGTAGCCTTGCCCTGATCAGGGGTTTCGGCGCAATGCTGGGCAAAACGcc       >  2:308940/1‑75 (MQ=255)                                              aaGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCAAAATGCTGGc    >  1:4093437/1‑76 (MQ=255)                                              aaGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGGTTTGGCGCAATGCTGGGCAAAATGCTGGc    >  2:536899/1‑76 (MQ=255)                                               aGCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCAAAAAGCTTGCa   >  2:4368938/1‑76 (MQ=255)                                                gCCGGTGTCGG‑‑CGGGACGCTCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCAAAATGCTGGCAg  >  2:3507356/1‑76 (MQ=255)                                                                    |                                                          GATTAATGCAAGGAATGCCGCTGGATAAAGTTATTGGCTCCATCAAAGCCGGTGTC‑G‑‑C‑GGACG‑TCGGTAGCCTTGCCCTGATCATGGGTTTTGGCGCAATGCTGGGCAAAATGCTGGCAG  >  NC_000913/3544301‑3544420

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑