Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,836,838	(C)5→4	coding (312/1335 nt)	adeQ ←	adenine permease AdeQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,836,834	0	C	.	97.7%	175.3 / ‑2.0	44	coding (316/1335 nt)	adeQ	adenine permease AdeQ
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base . (16/27);  total (16/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.17e-01

GGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATAC  >  NZ_CP009273/3836750‑3836923                                                                                     |                                                                                          ggATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGccccac                                                                                      >  1:600809/1‑88 (MQ=255) ggATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGccccac                                                                                      >  2:783866/1‑88 (MQ=255) ggATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGccccac                                                                                      >  2:567041/1‑88 (MQ=255) ggATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGccccac                                                                                      >  1:743039/1‑88 (MQ=255)         atcAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTTCGCCCAGCCCGGTCTGCCAGGAGATGCCCACCG‑TCccacgacctcga                                                                             <  2:469993/88‑1 (MQ=255)         aaCAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCccacgaccacga                                                                             <  2:889031/90‑1 (MQ=255)         aaCAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCccacgaccacga                                                                             <  1:567041/90‑1 (MQ=255)         aaCAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCccacgaccacga                                                                             <  2:343468/90‑1 (MQ=255)         aaCAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCccacgaccacga                                                                             <  2:741034/90‑1 (MQ=255)           cAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAg                                                                           <  2:829153/90‑1 (MQ=255)            aGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAgg                                                                          >  1:713002/1‑90 (MQ=255)             gCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGc                                                                         >  2:197791/1‑90 (MQ=255)             gCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGc                                                                         >  1:241464/1‑90 (MQ=255)             gCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGc                                                                         >  2:348566/1‑90 (MQ=255)             gCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGc                                                                         >  2:775326/1‑90 (MQ=255)                tGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCaaa                                                                      >  1:287917/1‑90 (MQ=255)                tGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCaaa                                                                      >  2:835088/1‑90 (MQ=255)                   gCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAaagaa                                                                   <  2:740637/90‑1 (MQ=255)                     aaaaaTAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAgg                                                                 <  1:835088/90‑1 (MQ=255)                       aaaTAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCg                                                               >  1:457617/1‑90 (MQ=255)                           aGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCa                                                           <  1:487712/90‑1 (MQ=255)                           aGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCa                                                           <  2:713002/90‑1 (MQ=255)                            gTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAgg                                                                 >  2:400296/1‑83 (MQ=255)                            gTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAgg                                                                 <  1:400296/83‑1 (MQ=255)                             tCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAg                                                          <  1:264838/90‑1 (MQ=255)                             tCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGc                                                         <  1:815470/90‑1 (MQ=255)                                 aCTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCa                                                     >  2:13613/1‑90 (MQ=255)                                            gAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGcc                                          <  1:163093/90‑1 (MQ=255)                                                  tGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGcc                                    <  1:503842/90‑1 (MQ=255)                                                   gcgcCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCa                                   <  1:50333/90‑1 (MQ=255)                                                   gcgcCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCa                                   <  1:383657/90‑1 (MQ=255)                                                     gcCCATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACg                                 >  2:821556/1‑90 (MQ=255)                                                      cccATCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACgg                                >  1:679900/1‑90 (MQ=255)                                                         aTCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTa                             <  2:477860/90‑1 (MQ=255)                                                          tCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTaa                            >  1:190225/1‑90 (MQ=255)                                                          tCCCGGTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTaa                            <  1:783866/90‑1 (MQ=255)                                                               gTCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAg                       <  2:679900/90‑1 (MQ=255)                                                                tCTGCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGc                      <  1:253035/90‑1 (MQ=255)                                                                   gCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTc                                                            <  2:185015/49‑1 (MQ=39)                                                                   gCCAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTc                                                            >  1:185015/1‑49 (MQ=39)                                                                     cAGGAGATGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAata                 <  2:203917/90‑1 (MQ=255)                                                                        gagaTGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATcc              <  1:161543/90‑1 (MQ=255)                                                                          gaTGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATcccc            <  2:640842/90‑1 (MQ=255)                                                                          gaTGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATcccc            <  1:251883/90‑1 (MQ=255)                                                                          gaTGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATcccc            <  1:225968/90‑1 (MQ=255)                                                                           aTGCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGACCCACCCCCACGGGAAAGTTAGCAAATATcccct           >  1:219673/1‑89 (MQ=255)                                                                             gCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGc                      <  2:641401/77‑1 (MQ=255)                                                                             gCCCATCG‑CCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGc                      >  1:641401/1‑77 (MQ=255)                                                                                     cccccACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATAc  <  2:340826/90‑1 (MQ=255)                                                                                     |                                                                                          GGATACGAAACAGCGTGAGCAAAAATAGTCCAACTGCGCCCCAGAATATTGCGCCCATCCCGGTCTGCCAGGAGATGCCCATCGCCCCCACGACCACGAAGGCAAAGAAGGCGTTCAGCCCCATTGCCGGAGCCAGCGCCACGGGTAAGTTAGCAAATATCCCCATCGCAATAC  >  NZ_CP009273/3836750‑3836923

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑