Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,297,289	A→T	12.7%	V41E (GTG→GAG)	TpbB ←	diguanylate cyclase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,297,289	0	A	T	12.7%	151.3 / 12.2	55	V41E (GTG→GAG)	TpbB	diguanylate cyclase
Reads supporting (aligned to +/- strand):  ref base A (29/19);  new base T (4/3);  total (33/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

GGCCACTTCTTCGGTACTGGCAATCAACGCCAGCGATTCGTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCATGGCTGCTCCGCCCGGCG  >  NC_002947/5297144‑5297427                                                                                                                                                  |                                                                                                                                            ggCCACTTCTTCGGTACTGGCAATCAACGCCAGCGATTCGTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGcc                                                                                                                                         <  1:551290/150‑1 (MQ=255)     aCTTCTTCGGTACTGGCAATCAACGCCAGCGATTCGTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGTGCTCGCCctgc                                                                                                                                     <  2:521969/150‑1 (MQ=255)          ttcGGTACTGGCAATCAACGCCAGCGATTCGTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGt                                                                                                                                <  2:683627/150‑1 (MQ=255)              gTACTGGCAATCAACGCCAGCGATTCGTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAgg                                                                                                                            <  2:809277/150‑1 (MQ=255)                  tGGCAATCAACGCCAGCGATTCGTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAgg                                                                                                                                  <  1:490733/140‑1 (MQ=255)                  tGGCAATCAACGCCAGCGATTCGTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAgg                                                                                                                                  >  2:490733/1‑140 (MQ=255)                            cGCCAGCGATTCGTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGATATGTGTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGGCAg                                                                                                              >  1:439226/1‑150 (MQ=255)                              ccAGCGATTCGTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGc                                                                                                            >  2:204063/1‑150 (MQ=255)                                   gATTCGTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACg                                                                                                       <  2:794562/150‑1 (MQ=255)                                        gTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAgg                                                                                                                            <  2:356253/124‑1 (MQ=255)                                        gTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAgg                                                                                                                            >  1:356253/1‑124 (MQ=255)                                        gTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGgcaag                                                                                                  >  1:613495/1‑150 (MQ=255)                                                          aTCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTg                                                                                >  2:81624/1‑150 (MQ=255)                                                           tCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTgg                                                                               >  2:271998/1‑150 (MQ=255)                                                              aaCACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCa                                                                           >  1:3833/1‑150 (MQ=255)                                                              aaCACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCa                                                                           >  1:628704/1‑150 (MQ=255)                                                                 accacAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCTCAGCAGGGTGAGGGACATACCCGCCAGGCGAACGGCAAGCAAGGCGACGCTCAGGTGG‑CCACgg                                                                        >  2:692322/1‑150 (MQ=255)                                                                   cacaGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATGGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGcc                                                                      >  2:485143/1‑150 (MQ=255)                                                                   cacaGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGcc                                                                      >  1:170467/1‑150 (MQ=255)                                                                   cacaGCCGCTTCTACGGTGTAGCTGATCGAGCGGGCGATCAACTGCAGGGTATGATTGTCATATACACGCAGGGCGAGCACGCCCAGCAGGGTGTGGGAGCTACCCCCCAGGCCACCGGCAAGCAAGGCGACGCTGAGCTGG‑CCACGGcc                                                                      >  2:377996/1‑150 (MQ=255)                                                                    acaGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCTGGGCGTGCTCGCCctgcgt                                                                                                                                   <  1:660270/89‑3 (MQ=255)                                                                    acaGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGccc                                                                     <  1:271998/150‑1 (MQ=255)                                                                           cTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGTCGCTGAGGTGG‑CCACGGCCCAGCACCg                                                              >  1:393601/1‑150 (MQ=255)                                                                           cTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCAccc                                                              >  2:763934/1‑149 (MQ=255)                                                                            ttCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGa                                                             <  2:170467/150‑1 (MQ=255)                                                                                aCGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAgcgc                                                         <  1:81624/150‑1 (MQ=255)                                                                                  ggTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATATACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAg                                                       >  2:121721/1‑150 (MQ=255)                                                                                        gTTGATCGCCCGCTCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGACACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGc                                                                  <  1:590932/133‑1 (MQ=255)                                                                                         ttGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCggg                                                >  2:150957/1‑150 (MQ=255)                                                                                             ccGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATTCCCGCAAGGAC‑ACGGCGGTGAAATCGGAGAGGGATTGGTCGACTGCCCAGCACCGAGCGCAGGGTCGGGCGCa                                            <  1:233856/149‑1 (MQ=255)                                                                                                 gCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGt                                        >  2:539503/1‑150 (MQ=255)                                                                                                  cGGTCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGTCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTa                                       <  1:320856/150‑1 (MQ=255)                                                                                                  cGGGCGATCAACTGCAGGTTATGGTTGGCATGGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTa                                       <  1:485143/150‑1 (MQ=255)                                                                                                         tCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGc                                >  2:227985/1‑150 (MQ=255)                                                                                                           aaCTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCgg                              <  1:204063/150‑1 (MQ=255)                                                                                                              tGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTc                           >  2:268960/1‑150 (MQ=255)                                                                                                              tGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTc                           <  1:268960/150‑1 (MQ=255)                                                                                                                   gTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCtt                      >  1:734699/1‑150 (MQ=255)                                                                                                                    atATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTc                     >  1:670573/2‑150 (MQ=255)                                                                                                                      aTGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCAt                   >  2:183284/1‑150 (MQ=255)                                                                                                                        ggTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGgc                                               >  2:215418/1‑120 (MQ=255)                                                                                                                        ggTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGgc                                               <  1:215418/120‑1 (MQ=255)                                                                                                                          ttGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCATGgct               <  2:613495/150‑1 (MQ=255)                                                                                                                            ggCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGTCAAGCAAGGCGACGCTGAGGTTT‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCATGgctgc             >  1:481426/1‑150 (MQ=255)                                                                                                                               aTAGACACGCAGGGCGAGCACGCCCAGCATGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCggg                                                >  2:620083/1‑112 (MQ=255)                                                                                                                               aTAGACACGCAGGGCGAGCACGCCCAGCATGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCggg                                                <  1:620083/112‑1 (MQ=255)                                                                                                                               aTAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCATGGCTGCTcc          <  2:628704/150‑1 (MQ=255)                                                                                                                                     acGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGAGCACGGTACGCTTGCGGGTCGGCGGCATGGTTGCTCCGCCCgg    >  2:7790/1‑150 (MQ=255)                                                                                                                                      tgctgggCGTGCTCGCCCTGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCATgg                 <  1:419699/132‑1 (MQ=255)                                                                                                                                      tgctgggCGTGCTCGCCCTGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCATgg                 >  2:419699/5‑136 (MQ=255)                                                                                                                                      tgctgggCGTGCTCGCCCTGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCATGGCTGCTCCGCCCGgc   >  1:804776/5‑150 (MQ=255)                                                                                                                                      tgctgggCGTGCTCGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCATGGCTGCTCCGCCCGgc   >  2:569034/5‑150 (MQ=255)                                                                                                                                       gcacagCGAGCACGCACAGCCCGGGGAGAGAACCACGCGCCACGCCAACGCCTAGCAAGGCGACGCTGACGGGG‑CCACGGCCCAGCACCGAGCGCAGTGTCGGGCGCACGGTACGCCTGCGGGTCGGGTTCATGGCTGCTCCGCCCGgcg  >  2:13513/6‑150 (MQ=255)                                                                                                                                       gCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCATGGCTGCTCCGCCCGgcg  >  2:741655/1‑150 (MQ=255)                                                                                                                                       cctgggCGTGCTCGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCATGGCTGCTCCGCCCGgcg  >  2:585836/4‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                            GGCCACTTCTTCGGTACTGGCAATCAACGCCAGCGATTCGTTGGCGGCGGCGCTGTCATCGAACACCACAGCCGCTTCTACGGTGTAGTTGATCGAGCGGGCGATCAACTGCAGGTTATGGTTGGCATAGACACGCAGGGCGAGCACGCCCAGCAGGGTGAGGGAGATACCCGCCAGGCCAACGGCAAGCAAGGCGACGCTGAGGTGG‑CCACGGCCCAGCACCGAGCGCAGGGTCGGGCGCACGGTACGCTTGCGGGTCGGCTTCATGGCTGCTCCGCCCGGCG  >  NC_002947/5297144‑5297427

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑