Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,537,061	A→T	10.8%	intergenic (+38/+65)	nadE → / ← PP_4870	NH(3)‑dependent NAD(+) synthetase/azurin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,537,061	0	A	T	10.8%	108.7 / 4.7	49	intergenic (+38/+65)	nadE/PP_4870	NH(3)‑dependent NAD(+) synthetase/azurin
Reads supporting (aligned to +/- strand):  ref base A (23/20);  new base T (2/3);  total (25/24)
Fisher's exact test for biased strand distribution p-value = 6.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.17e-01

CAGATCGATGCCTTCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTCACCACCGGCTTC  >  NC_002947/5536913‑5537206                                                                                                                                                       |                                                                                                                                                   cAGATCGATGCCTTCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCTGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGa                                                                                                                                                    <  1:159830/149‑1 (MQ=255) cAGATCGATGCCTTCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGa                                                                                                                                                    <  4:248954/149‑1 (MQ=255) cAGATCGATGCCTTCCTGCATGCGCAGCCGGGTGACCAGGCAGCGTTCGACATCATCGTCCCAACCTACCGCAAGACCCAGCACAAGGC‑‑CCTACTGCCTTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCTCGAATACGa                                                                                                                                                    <  4:56936/149‑1 (MQ=255)  aGATCGATGCCTTCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAg                                                                                                                                                   <  3:130256/149‑1 (MQ=255)   gATCGATGCCTTCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCAAGCACAAGCG‑‑CGAACTGCCGTTCGCTACTTGATAAGTGGCCTGCAGGAGCGGGTTAAACCGAGAATACCAgg                                                                                                                                                  >  7:139259/1‑149 (MQ=255)        aTGCCTTCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGaa                                                                                                                                             >  3:103087/1‑149 (MQ=255)         tGCCTTCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAAc                                                                                                                                            <  1:305369/149‑1 (MQ=255)           ccTTCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCTCGTATTCGCGGGTGAAccc                                                                                                                                          <  4:316754/149‑1 (MQ=255)             ttCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGt                                                                                                                                                >  8:336601/1‑141 (MQ=255)             ttCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGt                                                                                                                                                <  7:336601/141‑1 (MQ=255)                  gCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTAACCCGCGAATACGAGGGTGAACCCACCGACg                                                                                                                                   >  6:115807/1‑149 (MQ=255)                           gCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGGTAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCg‑g                                                                                                                         <  2:245953/149‑1 (MQ=25)                           gCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGTGTTCACCCTCGTATTCGCg‑g                                                                                                                         <  4:102320/149‑1 (MQ=25)                           gCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCg‑g                                                                                                                         <  4:103087/149‑1 (MQ=255)                           gCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAACACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTGCACCCGCTAATACGAGGGTGAACCCACCGAGGCATTCGCg‑g                                                                                                                         <  7:211273/149‑1 (MQ=255)                             cGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCG‑GGt                                                                                                                       <  1:329045/149‑1 (MQ=25)                               gTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCGGACGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTAACCCCCGAATACGAGGGTGAACCCCCCGACGCATTCGCC‑GGt                                                                                                                       >  1:109118/1‑149 (MQ=255)                                    ccAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCCCGCAAACGAGGGTGAACCCACCGACGCCTTCGCG‑GGTGGACCCg                                                                                                                >  3:228038/1‑149 (MQ=255)                                         cAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCt                                                                                                           <  2:309381/149‑1 (MQ=255)                                          aGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCg‑gg                                                                                                                        >  3:313676/1‑135 (MQ=255)                                          aGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCg‑gg                                                                                                                        <  4:313676/135‑1 (MQ=255)                                            cGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATATGGGGCCTGCAGGAGCGGGTTCACCCGCTAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCa                                                                                                        <  2:109118/149‑1 (MQ=255)                                              ttCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCTAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAgg                                                                                                      <  1:72069/149‑1 (MQ=255)                                                  aCATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGa                                                                                                                                                    <  7:36264/100‑1 (MQ=255)                                                  aCATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCAGCAGGAGCGGGTTCACCCGCGAATACGa                                                                                                                                                    >  8:36264/1‑100 (MQ=255)                                                      catcGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCg                                                                                              >  4:304403/1‑149 (MQ=255)                                                                 ccTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGcc                                                                                               <  7:268317/137‑1 (MQ=255)                                                                 ccTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGcc                                                                                               >  8:268317/1‑137 (MQ=255)                                                                    aCCGCCAGACCCACCACAAGCG‑‑CGAACTGCCGTTCGCGCCTTGATAAGTGGCCTGCAGGAGCGGGTGCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGtt                                                                                                   <  5:351730/130‑1 (MQ=255)                                                                        cAAGACCCTCCACAAGCG‑‑CTAACTCCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACtt                                                                             <  5:157152/148‑1 (MQ=255)                                                                        cAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTAACCCGCCAAATAGAGGGTGAAACCACCGACGCAATACCG‑GGTTAACCCCCAACAGCACGGTTAGCCGTGAGCCATTTATTACGTg                                                                            >  6:157152/1‑149 (MQ=255)                                                                        cAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTAACCCCCGAATAAGAGGGTGGACCCACCCACCCCATAGCG‑GGTGAAACCCCGCCTGCAGGGTTGGCCGGGAGCCGTTGATTaaatg                                                                            >  2:290605/1‑145 (MQ=255)                                                                        aaacaCCCAGCACCCGCG‑‑TGATCTGCGTTTCTCTCCTTTATCCGGGGCTTCCTGGTGGGTTTTCACCCCCTAATACCAGGGTTAACCCACCGACTC‑TTCGGGTGGTTACCCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTg                                                                            <  8:139259/145‑1 (MQ=255)                                                                                cgCACACGCG‑‑CTACCTGCCGTTCGCTCCTTGATACGGGGCCTGCAGGAGCGGGTTCACCCGCGAATCCGAGGGTGAACCCACCGACGCATTCGCG‑GGTTAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGAc                                                                    <  4:235124/148‑1 (MQ=37)                                                                                    caAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAAACCACCGACGCATTAGAG‑GGTGAACCCGCAACTGCACGGTTGGGCGGAAGCCGTTGAATACTTGTCGATGGACTTg                                                                >  1:304855/1‑149 (MQ=255)                                                                                            cgAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCTAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTtc                                                          <  1:290605/149‑1 (MQ=255)                                                                                                   cctttCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCTAATACGAGGGTTAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCatcatc                                                    <  7:189819/145‑1 (MQ=255)                                                                                                           tCCTTGATAAGTGGCCTGCAGGAGCGGGTTAACCCGCGAATACGAGGGTGAACCCACCGACGCATTAGCG‑GGTGAACCCGCTCCTGCAGGGTTCGGCGTCAGCCTTTGATTAATTGACGATGACCTTGCCGTTAATAATAGAGATGTgg                                           >  5:381171/1‑149 (MQ=38)                                                                                                                  tAAGTGGCCTGCAGGAGCGGGTTAACCCGCGAATACGAGGGTGAACCCACCGACGCATTAGCG‑GGTGAACCCGCTCCTGCAGGGTTAGCCGTCAGCCTTTGATTAATTGACGATGACCATTCCTTTCATAATCGAGATGTTGCCCggg                                     >  6:380364/1‑148 (MQ=38)                                                                                                                   aaGTGGCCTGCAGGAGCGGGTTCACCCGCGAAGACGTGGGTGCACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCGGCAGGGTTCGCCGGCAGCCTTTGATTACTTGACGATGACCTTGCCGTTCATCATCGAGATGTGGGCCggg                                     >  5:76428/1‑147 (MQ=38)                                                                                                                    aGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAg                                  <  3:304403/149‑1 (MQ=255)                                                                                                                                   cGGGTTCACCCGCTAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTg                   <  5:380364/149‑1 (MQ=255)                                                                                                                                      gTTCACCCGCGAATGCGTCGGTGGGTTCACCCTCGTATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAg                >  4:140949/1‑149 (MQ=21)                                                                                                                                      gTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGAtgt                                             <  7:74776/120‑1 (MQ=255)                                                                                                                                      gTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGAtgt                                             >  8:74776/1‑120 (MQ=255)                                                                                                                                            ccGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTcacca          >  2:79590/1‑149 (MQ=255)                                                                                                                                            ccGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTcacca          >  3:166663/1‑149 (MQ=255)                                                                                                                                            ccGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTcacca          >  5:129526/1‑149 (MQ=255)                                                                                                                                            ccGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTcacca          >  4:344597/1‑149 (MQ=255)                                                                                                                                            ccGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGAGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTcacca          >  2:87830/1‑149 (MQ=255)                                                                                                                                                 aaTACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTCACCACCGGc     >  1:180355/1‑149 (MQ=255)                                                                                                                                                     cGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTtc                                                          >  3:225264/1‑92 (MQ=255)                                                                                                                                                     cGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTtc                                                          <  4:225264/92‑1 (MQ=255)                                                                                                                                                      gAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTCACCACCGGCTTc  >  5:105706/1‑147 (MQ=255)                                                                                                                                                       |                                                                                                                                                   CAGATCGATGCCTTCCTGCATGGGCAGCCGGTTGACCAGGCAGCGTTCGACATCATCGTCGCCACCTACCGCAAGACCCAGCACAAGCG‑‑CGAACTGCCGTTCGCTCCTTGATAAGTGGCCTGCAGGAGCGGGTTCACCCGCGAATACGAGGGTGAACCCACCGACGCATTCGCG‑GGTGAACCCGCTCCTGCAGGGTTCGCCGTCAGCCTTTGATTACTTGACGATGACCTTGCCTTTCATCATCGAGATGTGGCCCGGGAAGGTGCAGAAGAAGCTGTAGTCACCACCGGCTTC  >  NC_002947/5536913‑5537206

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑