Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,050,088	Δ1 bp	7.7%	intergenic (+17/‑124)	PP_2662 → / → PP_2663	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,050,088	0	G	.	7.7%	157.4 / 8.1	52	intergenic (+17/‑124)	PP_2662/PP_2663	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (23/24);  new base . (2/2);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.68e-01

TGTTCCATGACATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCATAACGACGGT  >  NC_002947/3049941‑3050235                                                                                                                                                     |                                                                                                                                                    tGTTCCATGACATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAggc                                                                                                                                                   <  1:451519/150‑1 (MQ=255)       aTGACATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCCTA‑GCGGcccc                                                                                                                                             <  1:232161/150‑1 (MQ=255)         gACATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGa                                                                                                                                           >  1:1047917/1‑150 (MQ=255)                       ccTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCttt                                                                                                                             <  1:938996/150‑1 (MQ=255)                        cTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCtt                                                                                                                              >  2:358092/1‑148 (MQ=255)                        cTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCtt                                                                                                                              <  1:358092/148‑1 (MQ=255)                        cTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATAACTTTGCGGTGGGCGCGGTGTTGAAGTGGTAAGCGGACGGGGCCG‑GCATGCGGTGCCGAATAAAACGGGCtttt                                                                                                                            >  2:938996/1‑150 (MQ=255)                            aaCTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CGAGGCGGCCCCGAATGACACGGTCTTTTACGc                                                                                                                        <  1:1011407/150‑1 (MQ=255)                                ggtggCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCAt                                                                                                                    <  2:1333950/150‑1 (MQ=255)                                      cGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAAcc                                                                                                              <  2:1047917/150‑1 (MQ=255)                                          tACAACCAGTTTTCCATCGACGGGCATGACACCAGCGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGccc                                                                                                          >  1:366503/1‑150 (MQ=255)                                               ccAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCg                                                                                                     >  1:829195/1‑150 (MQ=255)                                                          tCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTa                                                                                          <  1:1133708/150‑1 (MQ=255)                                                                 gCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGaa                                                                                                                >  1:18066/1‑121 (MQ=255)                                                                 gCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGaa                                                                                                                <  2:18066/121‑1 (MQ=255)                                                                 gCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCg                                                                                   >  1:458634/1‑150 (MQ=255)                                                                    tggcacCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCTAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTca                                                                                <  2:442913/147‑1 (MQ=255)                                                                     gACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGt                                                                                  >  1:1078406/1‑147 (MQ=255)                                                                     gACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGt                                                                                  <  2:1078406/147‑1 (MQ=255)                                                                      acacCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGa                                                                                                                                           <  2:1275740/89‑1 (MQ=255)                                                                      acacCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGa                                                                                                                                           >  1:1275740/1‑89 (MQ=255)                                                                        acCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCAccc                                                                                                      <  1:197035/124‑1 (MQ=255)                                                                        acCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCAccc                                                                                                      >  2:197035/1‑124 (MQ=255)                                                                                   gAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGTCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCAcctcc                                                                 <  2:976662/150‑1 (MQ=255)                                                                                         aGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAAc                                                           >  2:1313786/1‑150 (MQ=255)                                                                                            cacCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGa                                                        >  2:280914/1‑150 (MQ=255)                                                                                             acCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCACCGAATGACACGGCCACATCCCATAAGTTGATCTCCGACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACATCCTTAAACTGAt                                                       >  1:324311/1‑150 (MQ=255)                                                                                                     cTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTcac                                                                               >  2:558730/1‑118 (MQ=255)                                                                                                     cTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTcac                                                                               <  1:558730/118‑1 (MQ=255)                                                                                                       ttGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCa                                             <  1:1313786/150‑1 (MQ=255)                                                                                                                gcgcGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCtttt                                                                                                                            <  1:1307115/62‑1 (MQ=255)                                                                                                                gcgcGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCtttt                                                                                                                            >  2:1307115/1‑62 (MQ=255)                                                                                                                             cTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATg                       >  2:557916/1‑150 (MQ=255)                                                                                                                             cTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATg                       >  1:427375/1‑150 (MQ=255)                                                                                                                              tGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATgc                      >  2:962358/1‑150 (MQ=255)                                                                                                                               ggTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATgca                     <  2:427375/150‑1 (MQ=255)                                                                                                                                gTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATgcag                    >  1:272017/1‑150 (MQ=255)                                                                                                                                  aaGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATgcagca                  <  2:829195/150‑1 (MQ=255)                                                                                                                                    gCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAgg                <  2:324311/150‑1 (MQ=255)                                                                                                                                      ggCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGga                                 >  2:787818/1‑131 (MQ=255)                                                                                                                                      ggCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGga                                 <  1:787818/131‑1 (MQ=255)                                                                                                                                      attcGGGGCCGCCTA‑GCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCt              >  1:64442/4‑150 (MQ=255)                                                                                                                                       gCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTc             <  1:280914/150‑1 (MQ=255)                                                                                                                                        tcGGGGCCGCCTA‑GCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTa                                                                                          >  1:95136/2‑72 (MQ=38)                                                                                                                                        tcGGGGCCGCCTA‑GCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTa                                                                                          <  2:95136/71‑1 (MQ=38)                                                                                                                                            ggCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTc                                                  <  2:1057421/108‑1 (MQ=255)                                                                                                                                            ggCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTc                                                  >  1:1057421/1‑108 (MQ=255)                                                                                                                                             gCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCATAacg       >  1:735839/1‑150 (MQ=255)                                                                                                                                              ccG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCATAacga      >  1:156933/1‑150 (MQ=255)                                                                                                                                                g‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGAt                                                       <  1:377113/99‑1 (MQ=255)                                                                                                                                                g‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGAt                                                       >  2:377113/1‑99 (MQ=255)                                                                                                                                                g‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCATAacgacg    <  1:731007/150‑1 (MQ=255)                                                                                                                                                   caGGCGGCCCCGAATGCCACGGTCTTTTACGCCCATGGACCCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAATCTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCATAACGACGgt  <  2:366503/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    TGTTCCATGACATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCG‑CTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCATAACGACGGT  >  NC_002947/3049941‑3050235

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: ‑