Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,762,990	A→T	10.7%	I64F (ATC→TTC)	PP_3326 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,762,990	0	A	T	10.7%	157.3 / 9.8	56	I64F (ATC→TTC)	PP_3326	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (24/26);  new base T (4/2);  total (28/28)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.57e-01

TCAGCGTCAACGCAGGCGCCCACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAA  >  NC_002947/3762844‑3763135                                                                                                                                                    |                                                                                                                                                   tCAGCGTCAACGCAGGCGCCCACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATcc                                                                                                                                                 >  1:1005661/1‑150 (MQ=255) tCAGCGTCAACGCAGGCGCCCACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATcc                                                                                                                                                 <  1:187300/150‑1 (MQ=255) tCAGCGTCAACGCAGGCGCCCACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCATGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATcc                                                                                                                                                 >  1:1115244/1‑150 (MQ=255)   aGCGTCAACGCAGGCGCCCACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCC‑AGGCGCTCGACCGTGACCGGGATCATGTTCCCg                                                                                                                                               <  2:216737/150‑1 (MQ=38)        cAACGCAGGCGCCCACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCAc                                                                                                                                          >  1:433469/1‑150 (MQ=255)             cAGGCGCCCACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCg                                                                                                                                     <  2:817711/150‑1 (MQ=255)                   cccACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑cc                                                                                                                              >  1:1216194/1‑150 (MQ=255)                    ccACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCt                                                                                                                             >  2:732100/1‑150 (MQ=255)                       cGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGc                                                                                                                          <  2:1216194/150‑1 (MQ=255)                                gACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGc                                                                                                                 <  2:768736/150‑1 (MQ=255)                                 aCCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGcc                                                                                                                >  1:1290517/1‑150 (MQ=255)                                    gaggagCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGtg                                                                                                             >  2:1009324/1‑150 (MQ=255)                                                      atCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCCGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCgcgc                                                                                                                      >  1:1368208/1‑120 (MQ=255)                                                      atCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCCGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCgcgc                                                                                                                      <  2:1368208/123‑4 (MQ=255)                                                       tCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATccc                                                                                                                                                <  2:846464/97‑1 (MQ=255)                                                       tCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATccc                                                                                                                                                >  1:846464/1‑97 (MQ=255)                                                       tCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGc                                                                                          >  2:533230/1‑150 (MQ=255)                                                         gAGGCCGTGTACGGCCACGGCGACGACAATAACAACTACAAAACGGAAAAGATCAAACGCGTCTGGGCGTTCGC‑CGTTACCGGGAAGATGATCCCGGTCACGGTCGATCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCt                                                                                        >  2:162634/1‑150 (MQ=255)                                                          aGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGa                                                                                                                                    <  1:38533/106‑1 (MQ=255)                                                          aGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGa                                                                                                                                    >  2:38533/1‑106 (MQ=255)                                                             ccGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCgg                                                                                    <  1:1260377/150‑1 (MQ=255)                                                              catgtACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGc                                                                                   <  2:1115244/148‑1 (MQ=255)                                                               gtgtACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCa                                                                                  >  2:226732/1‑150 (MQ=255)                                                                        cACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGtg                                                                         >  1:793950/1‑150 (MQ=255)                                                                        cACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGtg                                                                         <  2:1290517/150‑1 (MQ=255)                                                                            gcgcCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGtgctgc                                                                     <  2:433469/150‑1 (MQ=255)                                                                                 gAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTgctgct                                                                    >  2:1355291/1‑146 (MQ=255)                                                                                 gAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTgctgct                                                                    <  1:1355291/146‑1 (MQ=255)                                                                                       aaCGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACggg                                                          <  1:572329/150‑1 (MQ=255)                                                                                        atgCCTACAAGGGGGAAAAGATCAAGCGCGCCGGGGCGTTCGA‑CGTGACCGGGAACATGATCCCCGTCACGGTCGCGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGc                                                         <  2:572825/148‑1 (MQ=255)                                                                                          gCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTTACCGGGAACATGATCCCGGTCACGGAAGAGCG‑GCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCGGGACAACGGGCCt                                                       >  2:409313/1‑150 (MQ=255)                                                                                          gCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCt                                                       <  1:533230/150‑1 (MQ=255)                                                                                          gCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCt                                                       >  2:1415827/1‑150 (MQ=255)                                                                                            cTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTg                                                     <  1:732100/150‑1 (MQ=255)                                                                                                 aGGCGGAAAAGATCAAGCGCGCCTGGGCGTTTGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTcac                                                <  2:1041647/150‑1 (MQ=255)                                                                                                  ggCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTcaca                                               >  2:1243204/1‑150 (MQ=255)                                                                                                            aTCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGAc                                     >  2:579248/1‑150 (MQ=255)                                                                                                             tCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTg                                                     <  1:783135/133‑1 (MQ=255)                                                                                                             tCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTg                                                     >  2:783135/1‑133 (MQ=255)                                                                                                               aaGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAg                                  <  1:1009324/150‑1 (MQ=255)                                                                                                                   gcgcCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAAt                              <  2:540937/150‑1 (MQ=255)                                                                                                                     gcCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATgg                            <  1:1317718/150‑1 (MQ=255)                                                                                                                     cgccaggCGCTCGACCGTGACCGGGATCATGTTCCCGGTCAC‑GTCGAACGCCCAGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATg                             >  2:968532/6‑150 (MQ=21)                                                                                                                     cgccaggCGCTCGACCGTGACCGGGATCATGTTCCCGGTCAC‑GTCGAACG‑CCCGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATgg                            >  1:1305638/6‑150 (MQ=25)                                                                                                                      ccTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATggg                           <  1:579248/150‑1 (MQ=255)                                                                                                                        tGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTc                         >  1:822848/1‑150 (MQ=255)                                                                                                                              ttCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAg                                  >  2:1070119/1‑135 (MQ=255)                                                                                                                              ttCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAg                                  <  1:1070119/135‑1 (MQ=255)                                                                                                                                 gaccGTGACCGGGATCATGTTCCCGGTCAC‑GTCGAACGCCCAGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGa                 <  1:968532/147‑1 (MQ=37)                                                                                                                                     gTGACCGGGATCATGTTCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGc             >  1:856747/1‑150 (MQ=255)                                                                                                                                        aCCGGGATCATGTTCCCGGTCACGCGCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCAcc          >  1:903643/1‑150 (MQ=255)                                                                                                                                          cGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGcc                                                                                         <  2:129112/69‑1 (MQ=255)                                                                                                                                          cGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGcc                                                                                         >  1:129112/1‑69 (MQ=255)                                                                                                                                          cGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCa        <  1:226732/150‑1 (MQ=255)                                                                                                                                           gggAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCAt       >  2:644385/1‑150 (MQ=255)                                                                                                                                                cATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCaa  <  2:822848/150‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                   TCAGCGTCAACGCAGGCGCCCACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCATGTCAA  >  NC_002947/3762844‑3763135

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑