Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,762,985	A→T	10.7%	N62I (AAC→ATC)	PP_3326 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,762,985	0	A	T	10.7%	163.1 / 10.3	56	N62I (AAC→ATC)	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 = 7.60e-01

CCTGATGGTCAGCGTCAACGCAGGCGCCCACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCAT  >  NC_002947/3762836‑3763130                                                                                                                                                       |                                                                                                                                                   ccTGATGGCCAGGGTCAACTCAGGCGCCCACAGGCTGTGGACCGAGGAGCGACGTGGCAAAATCTAGGCCGTGTACCGCCACGGCTCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGaa                                                                                                                                                    <  2:465587/150‑1 (MQ=255)  cTGATGGTCAGCGTCAACGCAGGCGCCCACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAAc                                                                                                                                                   <  1:1265628/150‑1 (MQ=255)         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                                                               <  1:1355291/146‑1 (MQ=255)                                                                                         gAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTgctgct                                                               >  2:1355291/1‑146 (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                                                  >  2:1415827/1‑150 (MQ=255)                                                                                                  gCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCt                                                  <  1:533230/150‑1 (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)                                                                                                                                                       |                                                                                                                                                   CCTGATGGTCAGCGTCAACGCAGGCGCCCACGGCCTGTGGACCGAGGAGCGACGTGGCAATATCGAGGCCGTGTACGGCCACGGCGCCGAGGATAACGCCTACAAGGCGGAAAAGATCAAGCGCGCCTGGGCGTTCGA‑CGTGACCGGGAACATGATCCCGGTCACGGTCGAGCG‑CCTGGCGGATCATGCCGTGCTGCAACCACTTACCCCGCCTGCGGCACTTGCCGTGCTGCTGGACAACGGGCCTTGGTCACAGCGCCCGGACAAGCAATGGGTCAATCAGGATCGCACCCAT  >  NC_002947/3762836‑3763130

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: ‑