Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,584,941	G→T	11.1%	intergenic (+45/‑90)	benC → / → benD	benzoate 1,2‑dioxygenase electron transfer component/1,6‑dihydroxycyclohexa‑2,4‑diene‑1‑carboxylate dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,584,941	0	G	T	11.1%	155.3 / 6.7	54	intergenic (+45/‑90)	benC/benD	benzoate 1,2‑dioxygenase electron transfer component/1,6‑dihydroxycyclohexa‑2,4‑diene‑1‑carboxylate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base G (22/26);  new base T (4/2);  total (26/28)
Fisher's exact test for biased strand distribution p-value = 4.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.29e-01

CTGTGCGGCCCGCCACCCATGGTGGAAGCGGTCAGCCAGTACGTGCGTGAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGATTCCAAGGCAAGGTTGCCCTGGTCACCGGTGCCGCCCAAGGCATCG  >  NC_002947/3584792‑3585088                                                                                                                                                      |                                                                                                                                                    cTGTGCGGCCCGCCACCCATGGTGGAAGCGGTCAGCCAGTACGTGCGTGAGCAGGGCATTGCCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCg                                                                                                                                                     >  1:1011096/1‑150 (MQ=255)  tgtgCGGCCCGCCACCCATGGTGGAAGCGGTCAGCCAGTACGTGCGTGAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGa                                                                                                                                                    <  1:1205603/150‑1 (MQ=255)        gccagccaCCAATGGTGGAAGCGGTCAGCCAGTAAGTACGTGAGCAGCGCATTACAACGGCCAACTTCTAATACGAGCAGTTTGCGGATGCGGCATGACGCTCCCTGCTTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGc                                                                                                                                              >  2:1156787/1‑150 (MQ=255)             ccACCCATGGTGGAAGCGGTCAGCCAGTACGTGCGTGAGCAGGGCATTACCCCAGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCca                                                                                                                                         <  1:974451/150‑1 (MQ=255)                  cATGGTGGAAGCGGTCAGCCAGTACGTGCGTGAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCTCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCca                                                                                                                                         >  2:552223/1‑145 (MQ=255)                  cATGGTGGAAGCGGTCAGCCAGTACGTGCGTGAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCTCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCca                                                                                                                                         <  1:552223/145‑1 (MQ=255)                      gtggAAGCGGTCAGCCAGTACGTGCGTGAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATcg                                                                                                                                >  1:754741/1‑150 (MQ=255)                                    ccAGTACGTGCGTGAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAgg                                                                                                                  >  1:880746/1‑150 (MQ=255)                                        tACGTGCGTGAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCttt                                                                                                              <  1:1394593/150‑1 (MQ=255)                                        tACGTGCGTGAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCttt                                                                                                              <  1:91804/150‑1 (MQ=255)                                          cgtgcgtgAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGCGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGa                                                                                                            <  2:880746/150‑1 (MQ=255)                                           gtgcgtgAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCttt                                                                                                              <  2:983831/147‑1 (MQ=255)                                           gtgcgtgAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCttt                                                                                                              >  1:983831/1‑147 (MQ=255)                                               gtgAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAg                                                                                                                                      <  2:869792/119‑1 (MQ=255)                                               gtgAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAg                                                                                                                                      >  1:869792/1‑119 (MQ=255)                                                        gCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTtgct                                                                                              <  2:754741/150‑1 (MQ=255)                                                              ccccGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCcaca                                                                                        <  1:1054648/150‑1 (MQ=255)                                                               cccGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAg                                                                                       >  2:554850/1‑150 (MQ=255)                                                               cccGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAg                                                                                       >  1:33822/1‑150 (MQ=255)                                                               cccGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAg                                                                                       >  2:1079358/1‑150 (MQ=255)                                                                ccGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAgg                                                                                      <  2:1260702/150‑1 (MQ=255)                                                                ccGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAgg                                                                                      <  2:1079686/150‑1 (MQ=255)                                                                   gcaaaCTTCTCGTAGTAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGtc                                                                                   >  2:336058/4‑150 (MQ=39)                                                                       aCTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGtctctc                                                                               <  2:1638529/150‑1 (MQ=255)                                                                       aCTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGAGCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGtctctc                                                                               >  1:1419535/1‑150 (MQ=255)                                                                             actacGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCTCGCGCGCTCCcaca                                                                                                                                       <  2:407361/88‑1 (MQ=38)                                                                             actacGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCTCGCCCGCTCCcaca                                                                                                                                       >  1:407361/1‑88 (MQ=255)                                                                              ctacGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGt                                                                                    <  2:737083/138‑1 (MQ=255)                                                                              ctacGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGt                                                                                    >  1:737083/1‑138 (MQ=255)                                                                               tacGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTg                                                                       <  1:1079358/150‑1 (MQ=255)                                                                                      aGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGAttt                                                                <  1:554850/150‑1 (MQ=255)                                                                                        tttGCGGCTGCGGCCTGACGCTCCCTTATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTAc                                                              <  1:1376697/150‑1 (MQ=255)                                                                                                      cTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGa                                                >  1:1341872/1‑150 (MQ=255)                                                                                                       tGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGAt                                               >  2:316298/1‑150 (MQ=255)                                                                                                           gCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGaa                                                                          <  2:21500/119‑1 (MQ=255)                                                                                                           gCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGaa                                                                          >  1:21500/1‑119 (MQ=255)                                                                                                              cccTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGATTCcaagg                                        <  2:33822/150‑1 (MQ=255)                                                                                                                cTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGATTCcaaggca                                      >  1:489048/1‑150 (MQ=255)                                                                                                                       aaaGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTACCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGAtt                                                                 <  2:931270/116‑1 (MQ=255)                                                                                                                       aaaGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTACCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGAtt                                                                 >  1:931270/1‑116 (MQ=255)                                                                                                                           cAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAaga                                                                                                      <  2:310898/75‑1 (MQ=255)                                                                                                                           cAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAaga                                                                                                      >  1:310898/1‑75 (MQ=255)                                                                                                                              tACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGtctct                                                                                >  1:124175/1‑94 (MQ=255)                                                                                                                              tACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGtctct                                                                                <  2:124175/94‑1 (MQ=255)                                                                                                                                   cGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGaacaa                                                    >  1:847064/1‑117 (MQ=255)                                                                                                                                   cGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGaacaa                                                    <  2:847064/117‑1 (MQ=255)                                                                                                                                     aCCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGATTCCAAGGCAAGGTTGCCCTGGTCACCGGTg                 <  2:1011096/150‑1 (MQ=255)                                                                                                                                           tgGGAGCGGGCTCGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGATTCCAAGGCAAGGTTGCCCTGGTCACCGGTGCCGccc           >  2:1347866/1‑150 (MQ=255)                                                                                                                                             ggAGCGGGCTCGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGATTCCAAGGCAAGGTTGCCCTGGTCACCGGTGCCGCCCaa         >  2:139145/1‑150 (MQ=255)                                                                                                                                              gAGCGGGCTCGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGAt                                                                  <  1:874552/92‑1 (MQ=255)                                                                                                                                              gAGCGGGCTCGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGAt                                                                  >  2:874552/1‑92 (MQ=255)                                                                                                                                                  gggCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGATTCCAAGGCAAGGTTGCCCTGGt                         <  2:949647/129‑1 (MQ=255)                                                                                                                                                  gggCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGATTCCAAGGCAAGGTTGCCCTGGt                         >  1:949647/1‑129 (MQ=255)                                                                                                                                                   ggCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGATTCCAAGGCAAGGTTGCCCTGGTCACCGGTGCCGCCCAAGGCATc   <  1:1115334/150‑1 (MQ=255)                                                                                                                                                    gCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTCAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGATTCCAAGGCAAGGTTGCCCTGGTCACCGGTGCCGCCCAAGGCATCg  >  1:195198/1‑150 (MQ=255)                                                                                                                                                      gAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTa                                                               >  1:433266/1‑87 (MQ=255)                                                                                                                                                      gAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTa                                                               <  2:433266/87‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                    CTGTGCGGCCCGCCACCCATGGTGGAAGCGGTCAGCCAGTACGTGCGTGAGCAGGGCATTACCCCGGCCAACTTCTACTACGAGAAGTTTGCGGCTGCGGCCTGACGCTCCCTGATTCAAAGCAATACGCCGACCCTGTGGGAGCGGGCGAGCCCGCTCCCACAGTGATCGCGCAGCCTTTCAGGCTTTGAGCAAGAGAGTTGCTGCCACAGGGTCTCTCGCGAACTGGAGATTTACATATGAACAACAGATTCCAAGGCAAGGTTGCCCTGGTCACCGGTGCCGCCCAAGGCATCG  >  NC_002947/3584792‑3585088

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