Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,910,911	C→A	14.7%	E239* (GAG→TAG)	atpG ←	F1 sector of membrane‑bound ATP synthase, gamma subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,910,911	0	C	A	14.7%	123.4 / 4.2	46	E239* (GAG→TAG)	atpG	F1 sector of membrane‑bound ATP synthase, gamma subunit
Reads supporting (aligned to +/- strand):  ref base C (18/21);  new base A (3/4);  total (21/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-01

CACCTCAAGAGCATCGTACACGCGCGGTACGGCATCCTGAGGGAATTCGACGTCAACTACGGCGCCGATTACCTGGACAATCTTTCCAGTAGCCATCTTAAATCCTCTACGAAATAACCTGTTTAAACCGCGGCGGCCCCCGAGACGATCTCGGTGAGTTCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCGGGTTCGTACAGGTAATCCCAGGATTTATGTTTCAGATCATCATCATCTGATGCCGGTAACGGCAGCAGCTGGCTGATGGTCGGAACCTGAGACATGGTGTTAATAAATTTGTTGCTGACAATGTAAAGCTTGTCCAGACGGCCTTCGTCGTAGGCCTGCAACATCAC  >  CP009273/3910640‑3911163                                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                             cACCTCAAGAGCATCGTACACGCGCGGTACGGCATCCTGAGGGAATTCGACGTCAACTACGGCGCCGATTACCTGGACAATCTTTCCAGTAGCCATCTTAAATCCTCTACGAAATAACCTGTTTAAACCGCGGCGGCCCCCGAGACGATCTCAGTGAGTTCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATGCCAACTGCAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTccc                                                                                                                                                                                                                                                            >  1:622138/1‑272 (MQ=255)                                      tGAGGGAATTCGACGTCAACTACGGCGCCGATTACCTGGACAATCTTTCCAGTAGCCATCTTAAATCCTCTACGAAATAACCTGTTTAAACCGCGGCGGCCCCCGAGACGATCTCGGTGAGTTCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTgaca                                                                                                                                                                                                                       >  1:88279/1‑272 (MQ=255)                                                                                               aTCTTAAATCCTCTACGAAATAACCTGTTTAAACCGCGGCGGCCCCCGAGACGATCTCGGTGAGTTCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCATGATAAACCTGAGATTCGACATa                                                                                                                                                                                                              >  1:397498/1‑226 (MQ=255)                                                                                               aTCTTAAATCCTCTACGAAATAACCTGTTTAAACCGCGGCGGCCCCCGAGACGATCTCGGTGAGTTCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCAGGCTGCCGCCATTGTAGGTCGCGGCTTTCATCGCCACAATACGGGCGGCCTGCTCGCTGGcc                                                                                                                                                                                                                                                       <  1:162104/185‑1 (MQ=255)                                                                                                   tAAATCCTCTACGAAATAACCTGTTTAAACCGCGGCGGCCCCCGAGACGATCTCGGTGAGTTCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCATGATAAACCTGAGATTCGACATAacga                                                                                                                                                                                                          <  2:397493/226‑1 (MQ=255)                                                                                                                          tttAAACCGCGGCGGCCCCCGAGACGATCTCGGTGAGTTCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTATTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACgc                                                                                                                                                                                                       >  2:63682/1‑206 (MQ=255)                                                                                                                              aaCCGCGGCGGCCCCCGAGACGATCTCGGTGAGTTCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTATTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACgcagca                                                                                                                                                                                                   <  1:63682/206‑1 (MQ=255)                                                                                                                                    ggcggcCCCCGAGACGATCTCGGTGAGTTCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCATGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTTGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCGGGTTCGTACAGGTAATCCCAGGATTTATGTTTCAGATCATCATCATCTg                                                                                                                        >  1:262922/1‑275 (MQ=255)                                                                                                                                       gtatatgagtcagATCTCGGTGAGTTCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCAGGCTGCCGNCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCGGGTTCGTACAGGTAATCCCAGGACTTATGTTTCAGATCATCATCATCTGATg                                                                                                                     <  1:468944/263‑1 (MQ=255)                                                                                                                                                               ttCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTTGCGGCTTTCATCGCCACCATACGGGCGGCATGCTCGCTGGCCAGGTGTTCAACCCCGCCCTGATAAACCTGAGATTCCACATAACGAAGCCGAAGGGTATCCAGCAACGCCCTCGGACAGGGTTCGCTCAGGCAACGCAAGGATTTAAGTTCAAGATCATAGTAAGCTGTTTCCGGTCACgttcttgccacttg                                                                                               >  2:468937/1‑260 (MQ=255)                                                                                                                                                                     aGTAATGCTGGCTTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCAGGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCGGGTTCGTACAGGTAATCCCAGGATTTATGTTTCAGATCATCATCATCTGATGCCGGTAACGGCAGCAGCTGGCTGATGGTCg                                                                                       <  1:580976/275‑1 (MQ=255)                                                                                                                                                                         aTGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAac                                                                                                                                                                                                            >  1:576075/1‑154 (MQ=255)                                                                                                                                                                             tGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAacgacg                                                                                                                                                                                                        <  2:576064/154‑1 (MQ=255)                                                                                                                                                                                                           gCAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTga                                                                                                                                                                                                                         >  2:483454/1‑107 (MQ=255)                                                                                                                                                                                                            cAGCTCTTTAATCAGGCTGCCGCTATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGCTCGGGTTCGTACAGGTAATCCCAGGAtt                                                                                                                                                <  1:507311/179‑1 (MQ=255)                                                                                                                                                                                                            cAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCg                                                                                                                                                                                                                                                             <  2:368685/70‑1 (MQ=255)                                                                                                                                                                                                             aGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCGACCATACGGGCGGCCTGCTAGCTGGCCAgg                                                                                                                                                                                                                                                    >  1:621530/1‑78 (MQ=255)                                                                                                                                                                                                               ctctTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGAtt                                                                                                                                                                                                                     <  1:483462/107‑1 (MQ=255)                                                                                                                                                                                                               ctctTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCGGGTTCGTACAGGTAATCCCAGGATTTATGTTTCAGATCATCATCATCTGATGCCGGTAACGGCAGCAGCTGGCTGATGGt                                                                                         >  1:131250/1‑231 (MQ=255)                                                                                                                                                                                                               ctctTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCGGGTTCGTACAGGTAATCCCAGGATTTATGTTTCAGATCATCATCATCCGATGCCGGTAACGGCAGCAGCTGGCTGATGGt                                                                                         <  2:131249/231‑1 (MQ=255)                                                                                                                                                                                                                 ctTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCa                                                                                                                                                                                                                                              >  1:367762/1‑80 (MQ=255)                                                                                                                                                                                                                 ctTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTAGCTGGCCAGGtttt                                                                                                                                                                                                                                                <  2:621519/78‑1 (MQ=255)                                                                                                                                                                                                                     aaTCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCg                                                                                                                                                                                                                                                             <  1:61561/61‑1 (MQ=255)                                                                                                                                                                                                                     aaTCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCa                                                                                                                                                                                                                                          <  2:367757/80‑1 (MQ=255)                                                                                                                                                                                                                           gCTGCCGCCATTGTCGGTAGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTAGCTGGCCAGGTTTTCAACCACGccc                                                                                                                                                                                                                                     >  2:529422/1‑79 (MQ=255)                                                                                                                                                                                                                            cTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTAGCTGGCCAGGTTTTCAAc                                                                                                                                                                                                                                            >  1:51540/1‑71 (MQ=255)                                                                                                                                                                                                                               ccgccATTGTCGGTAGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTAGCTGGCCAGGTTTTCAACCACGCCCTGAt                                                                                                                                                                                                                                 <  1:529433/79‑1 (MQ=255)                                                                                                                                                                                                                                cgccATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTAGCTGGCCAGGTTTTCAACCACg                                                                                                                                                                                                                                        <  2:51540/71‑1 (MQ=255)                                                                                                                                                                                                                                     ttGTCGTTCGCGGCTTACATCGCCACCATACGGGCGGCCTGCTCACTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGa                                                                                                                                                                            >  1:497304/1‑126 (MQ=255)                                                                                                                                                                                                                                     ttGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACgc                                                                                                                                                                                                       >  2:43219/1‑99 (MQ=255)                                                                                                                                                                                                                                         cggtcgCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACgcagca                                                                                                                                                                                                   <  1:43219/99‑1 (MQ=255)                                                                                                                                                                                                                                         cggtcgCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCgg                                                                                                                                                                        <  2:497296/126‑1 (MQ=255)                                                                                                                                                                                                                                             cgcgGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTc                                                                                                                                                                               >  1:101525/1‑115 (MQ=255)                                                                                                                                                                                                                                                 gCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGAt                                                                                                                                                                           <  2:101524/115‑1 (MQ=255)                                                                                                                                                                                                                                                          gCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGa                                                                                                                                                                            >  2:478520/1‑105 (MQ=255)                                                                                                                                                                                                                                                           gcaaaattcGGGGGGCCTGCTAGCTGGCTAGGTTTTCAACCAAGCCCTGATTAACCTGAGATTCGAAATGACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCGGGTTCGTACAGGTAATCCCAGGATTTATGTTTCAGATCATCATCATCTGATGCCGGTAACGGCAGCAGCTGGCTGATGGTCGGAACCTGAGACATGGTGTTAATAAATTTGTTGCTGACAATGTAAAGCTTGTCCAGACGGCCTTCGTCGTAGGCCTGCAACATCAc  <  2:622127/266‑1 (MQ=255)                                                                                                                                                                                                                                                              ccaTACGGGCTGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATc                                                                                                                                                                          >  2:256050/1‑103 (MQ=255)                                                                                                                                                                                                                                                              ccaTACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCCACGCCTTCGGATCgg                                                                                                                                                                        <  1:478528/105‑1 (MQ=255)                                                                                                                                                                                                                                                               caTACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACAt                                                                                                                                                                                                               >  1:559823/1‑65 (MQ=255)                                                                                                                                                                                                                                                                  aCGGGCTGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCGGGt                                                                                                                                                                      <  1:256054/103‑1 (MQ=255)                                                                                                                                                                                                                                                                   cGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAacg                                                                                                                                                                                                           <  2:559812/65‑1 (MQ=255)                                                                                                                                                                                                                                                                         gcCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAac                                                                                                                                                                                                            >  2:575826/1‑58 (MQ=255)                                                                                                                                                                                                                                                                         gcCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACgc                                                                                                                                                                                                       >  1:357312/1‑63 (MQ=255)                                                                                                                                                                                                                                                                          ccTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATCACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCGGGTTCGTACAGGTAATCCCAGGATTTATGTTTCAGatc                                                                                                                                   >  1:109274/1‑130 (MQ=255)                                                                                                                                                                                                                                                                             gCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAacgacg                                                                                                                                                                                                        <  1:575837/58‑1 (MQ=255)                                                                                                                                                                                                                                                                             gCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACgcagca                                                                                                                                                                                                   <  2:357307/63‑1 (MQ=255)                                                                                                                                                                                                                                                                              cTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCGGGTTCGTACAGGTAATCCCAGGATTTATGTTTCAGatcatca                                                                                                                               <  2:109273/130‑1 (MQ=255)                                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                             CACCTCAAGAGCATCGTACACGCGCGGTACGGCATCCTGAGGGAATTCGACGTCAACTACGGCGCCGATTACCTGGACAATCTTTCCAGTAGCCATCTTAAATCCTCTACGAAATAACCTGTTTAAACCGCGGCGGCCCCCGAGACGATCTCGGTGAGTTCCTGAGTAATGCTGGCCTGACGAGCTTTGTTGTATACCAACTGCAGCTCTTTAATCAGGCTGCCGCCATTGTCGGTCGCGGCTTTCATCGCCACCATACGGGCGGCCTGCTCGCTGGCCAGGTTTTCAACCACGCCCTGATAAACCTGAGATTCGACATAACGACGCAGCAGGGTATCCAGCAACGCCTTCGGATCGGGTTCGTACAGGTAATCCCAGGATTTATGTTTCAGATCATCATCATCTGATGCCGGTAACGGCAGCAGCTGGCTGATGGTCGGAACCTGAGACATGGTGTTAATAAATTTGTTGCTGACAATGTAAAGCTTGTCCAGACGGCCTTCGTCGTAGGCCTGCAACATCAC  >  CP009273/3910640‑3911163

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑