Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,741,564	A→T	9.2%	intergenic (‑179/+49)	PP_5038 ← / ← PP_5039	lipoprotein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,741,564	0	A	T	9.2%	150.0 / 7.1	55	intergenic (‑179/+49)	PP_5038/PP_5039	lipoprotein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (31/18);  new base T (3/2);  total (35/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.85e-01

GAGTGGCCTGCAGTGACCTTCGACGTGAAAATCCCTCCCAGGTTCCCTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTTGCGGTGCGGGAAGCGCCCGAAGCGGGC  >  NC_002947/5741416‑5741711                                                                                                                                                      |                                                                                                                                                    gAGTGGCCTGCAGTGACCTTCGACGTGAAAATCCCTCCCAGGTTCCCTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCAATTAATCACAAAGCATTAATCCTGCGCCCAATAAAAAAGGCCGCC‑CCCAAt                                                                                                                                                    <  1:447540/150‑1 (MQ=255)       ccTGCAGTGACCTTCGACGTGAAAATCCCTCCCAGGTTCCCTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCT‑CCCATTgggggc                                                                                                                                              >  2:760017/1‑147 (MQ=255)        cTGCAGTGACCTTCGACGTGAAAATCCCTCCCAGGTTCCCTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCCTTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCg                                                                                                                                             >  1:190912/1‑150 (MQ=255)         tGCAGTGACCTTCGACGTGAAAATCCCTCCCAGGTTCCCTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCT‑CCCATTGGGGGCgg                                                                                                                                            <  1:760017/150‑1 (MQ=255)               gACCTTCGACGTGAAAATCCCTCCCAGGTTCCCTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGc                                                                                                                                      >  2:829704/1‑150 (MQ=255)                  cTTCGACGTGAGAATCCCTCCCAGGGTACCTGGCCCACCCCCTATGTCCCTCAACCAATGGTCGGCTGGCCCCTACTGTGCGCTTCATCACCAACCATTAATCATGCGCCCAATCACAAAGGCCGCC‑CCCACTGGCAGCGGCCttcggcg                                                                                                                                   >  2:328191/1‑145 (MQ=255)                           gAAAATCCCTCCCAGGTTCCCTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATAGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCt                                                                                                                          <  1:263721/150‑1 (MQ=255)                                   ctcccAGGTTCCCTGCCCCACCCCCTATCTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCAcagca                                                                                                                  >  1:157269/1‑150 (MQ=255)                                    tcccAGGTTCCCTGCCCCACCCCCTATGTCCCTACACCATGGTTCGAATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAGAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCAcagcag                                                                                                                 >  1:747247/1‑150 (MQ=255)                                     cccAGGTTCCCTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAgg                                                                                                                <  2:157269/150‑1 (MQ=255)                                        aGGTTCCCTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGccc                                                                                                             >  2:791704/1‑150 (MQ=255)                                             cccTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTgg                                                                                                        <  1:210288/150‑1 (MQ=255)                                               cTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGc                                                                                                      >  2:405963/1‑150 (MQ=255)                                               cTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGc                                                                                                      >  2:564488/1‑150 (MQ=255)                                                    ccACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAg                                                                                                 >  1:503131/1‑150 (MQ=255)                                                      aCCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAAt                                                                                                                                                    <  1:39601/97‑1 (MQ=255)                                                      aCCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAAt                                                                                                                                                    >  2:39601/1‑97 (MQ=255)                                                         cccTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCCATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCg                                                                                            >  1:482290/1‑150 (MQ=255)                                                         cccTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCg                                                                                            >  2:651790/1‑150 (MQ=255)                                                            tATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGa                                                                                         >  1:591724/1‑150 (MQ=255)                                                             aTGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGAc                                                                                        >  2:35632/1‑150 (MQ=255)                                                               gTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAg                                                                                                                                               <  1:654910/93‑1 (MQ=255)                                                               gTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAg                                                                                                                                               >  2:654910/1‑93 (MQ=255)                                                                tCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCa                                                                                     <  2:155288/150‑1 (MQ=255)                                                                  ccTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGGCGCCGCACCATGGG‑GCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAgg                                                                                   >  1:270528/1‑150 (MQ=255)                                                                  ccTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAgg                                                                                   >  1:361720/1‑150 (MQ=255)                                                                   cTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTCCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGc                                                                                  >  1:815029/1‑150 (MQ=255)                                                                      cacCATTGGTCGGATGGCGACTCCTGTGCGATTAATCACAAAGCATTAATCATGCTCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTcc                                                                               <  2:108965/150‑1 (MQ=255)                                                                               tCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAg                                                                      <  1:356142/150‑1 (MQ=255)                                                                                 ggATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGc                                                                                                      <  2:220059/116‑1 (MQ=255)                                                                                 ggATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGc                                                                                                      >  1:220059/1‑116 (MQ=255)                                                                                               gtgCGATTAATCACAAAGCATTAATCATGCGACCCATAACCTAGGCGGCC‑ACGAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTgg                                                      <  2:401308/150‑1 (MQ=255)                                                                                                tgCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGt                                                     >  1:484267/1‑150 (MQ=255)                                                                                                  cGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGc                                                   >  1:578352/1‑150 (MQ=255)                                                                                                    aTTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTc                                                 <  2:578352/150‑1 (MQ=255)                                                                                                          cacaAAGCATTAATCATGCGCCCAATAAAAAAGGACGAA‑TTCAATGCGACAACGGGTGCGGCGCGAGGCCGGCACATCAGGCCCCTTGGGCCTCAGAACCGGAACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGc                                           >  1:15950/1‑150 (MQ=255)                                                                                                           acaAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCt                                          >  2:776738/1‑150 (MQ=255)                                                                                                            caAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTc                                         <  1:651790/150‑1 (MQ=255)                                                                                                                      aTCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAgg                               >  1:481767/1‑150 (MQ=255)                                                                                                                       tCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGt                              >  2:808573/1‑150 (MQ=255)                                                                                                                         aTGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGGCCCTTGGGCCTCAGAACCGGGACGCAGGCTCAAGCAAAAATTCCATTTCTTCGCTGGTTCTCGGCCGTTCCAGCACCAGGTtg                            <  2:190912/150‑1 (MQ=255)                                                                                                                         aTGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTtg                            >  2:551481/1‑150 (MQ=255)                                                                                                                                cAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTtgcggtgcg                     <  2:484267/150‑1 (MQ=255)                                                                                                                                   tAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTTGCGGTGCGGGa                  >  1:562927/1‑150 (MQ=255)                                                                                                                                     aaaaaGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTTGCGGTGCGGGAAg                >  2:178681/1‑150 (MQ=255)                                                                                                                                      aaaaGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTTGCGGTGCGGGAAgc               >  2:342947/1‑150 (MQ=255)                                                                                                                                        aaGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTtgcggtgc                      >  1:86460/1‑141 (MQ=255)                                                                                                                                        aaGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTtgcggtgc                      <  2:86460/141‑1 (MQ=255)                                                                                                                                        aaGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTTGCGGTGCGGGAAgcgc             >  2:834890/1‑150 (MQ=255)                                                                                                                                           gccgct‑CCCATTGGGGGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCaaaaa                                                                       <  1:704875/89‑1 (MQ=39)                                                                                                                                           gccgct‑CCCATTGGGGGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCaaaaa                                                                       >  2:704875/1‑89 (MQ=39)                                                                                                                                            acctttcccATTGGGGGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCACTGGTGCTCGACCGCTCCAGCACCAGGTTGCGGTGCGGGAAGCGCCCg          >  1:247250/7‑150 (MQ=255)                                                                                                                                              gcc‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGACCCTTGGGCCTCAGAACCGGGACCCAGGGTTCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTTGCGGTGCGGGAAGCGCCCGAAg       <  1:405963/150‑1 (MQ=255)                                                                                                                                                   ccAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCCATTCGCTTGTGCTCGGCCGCTCCAGCACCAGGTTGCGGTGCGGGAAGCGCCCGAAGCggg   <  2:503131/150‑1 (MQ=255)                                                                                                                                                    cAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTTGCGGTGCGGGAAGCGCCCGAAGCGGGc  >  2:472005/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                    GAGTGGCCTGCAGTGACCTTCGACGTGAAAATCCCTCCCAGGTTCCCTGCCCCACCCCCTATGTCCCTACACCATTGGTCGGATGGCCACTACTGTGCGATTAATCACAAAGCATTAATCATGCGCCCAATAAAAAAGGCCGCC‑CCCAATGGGAGCGGCCTTGCGTCGCGATGCCTGCACAGCAGGCCCCTTGGGCCTCAGAACCGGGACCCAGGCTCCAGCAAAAAGTCCATCTCTTCGCTGGTGCTCGGCCGCTCCAGCACCAGGTTGCGGTGCGGGAAGCGCCCGAAGCGGGC  >  NC_002947/5741416‑5741711

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: ‑