Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,063,201	G→A	10.8%	intergenic (+58/‑149)	PP_1838 → / → PP_1839	membrane protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,063,201	0	G	A	10.8%	120.7 / 5.4	48	intergenic (+58/‑149)	PP_1838/PP_1839	membrane protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (21/20);  new base A (2/3);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.66e-01

TGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTC  >  NC_002947/2063055‑2063348                                                                                                                                                      |                                                                                                                                                     tGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑Aggg                                                                                                                                                    <  1:69806/149‑1 (MQ=255)  gCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGt                                                                                                                                                   >  2:89890/1‑149 (MQ=255)     cAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCGCACAGGACCTGCAC‑‑AAGGtcc                                                                                                                                                 >  6:167251/1‑146 (MQ=38)       agaagCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGa                                                                                                                                              >  7:48603/1‑149 (MQ=255)        gaagCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGAc                                                                                                                                             >  7:118397/1‑149 (MQ=255)                  gCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAgg                                                                                                                                   <  5:14433/149‑1 (MQ=255)                   cGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGt                                                                                                                                  <  8:118397/149‑1 (MQ=255)                       tatCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAACGGAAACCCGGGCCGCCTTGCGGCCCAATAGCCGGCATTCCCGCACCCACACGCATTTCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCt                                                                                                                               >  1:215839/1‑149 (MQ=255)                       tatCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCGCACAGGACCTGCAC‑‑AAGGTCCGAACCCTGTGCaatgcct                                                                                                                               <  6:163128/148‑7 (MQ=21)                         tCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCCCAGGCATTGCAC‑‑ACGGTGCGGTCCATGGGCCGGTCCagtg                                                                                                                            >  6:220229/1‑149 (MQ=255)                         tCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGTTTCGGACCTTGTGCAGGTCCtgtg                                                                                                                            <  3:215874/149‑1 (MQ=255)                         tCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCtgt                                                                                                                             <  5:269250/148‑1 (MQ=255)                          ccAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTtgtg                                                                                                                                       >  8:111538/1‑137 (MQ=255)                          ccAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTtgtg                                                                                                                                       <  7:111538/137‑1 (MQ=255)                               ccGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCGCACAGGACCTGCAC‑‑AAGGTCCGAACCCTGTGCAATGCCTGTGGGAGCg                                                                                                                      <  5:167251/149‑1 (MQ=18)                               ccGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCg                                                                                                                      <  2:112722/149‑1 (MQ=255)                               ccGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTAGCGGGCTTGCCCGCTCCCCCCGGCCTTGCAC‑‑AGGGTTCGGGCCTTTTGCAGGTCCAGTGcgcgcg                                                                                                                      >  7:160719/1‑149 (MQ=255)                                            ccTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGCGCGGGCAAGCCcgcg                                                                                                          >  5:55721/1‑148 (MQ=255)                                              gcgtgGAAAACACCGCCGCGGGGGTCCACGCAACACCTAA‑TAAACCCGGGGCCGCGTGGCGCCCAATTCGCGGGCTTGCCCGCTCCCACCGCCTTGCCAC‑‑AGGGTCCGCCCTTTGTGCTGGTCCTGGGCGCGCGGGCAAGCCCGCGaa                                                                                                        <  8:144485/145‑1 (MQ=255)                                               gctgGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTAGGCCCGTGTGCAGGTGCGGTGCGCGCGGGCAAGCCcgcgca                                                                                                        >  7:144485/1‑145 (MQ=38)                                                ctgGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAAt                                                                                                       <  8:48603/147‑1 (MQ=255)                                                ctgGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATg                                                                                                      <  2:215839/148‑1 (MQ=255)                                                   gATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCGCCCCCCGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGcc                                                                                                  >  2:186001/1‑149 (MQ=255)                                                     tAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATgg                                                                                                     >  5:127556/1‑144 (MQ=255)                                                     tAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATgg                                                                                                     <  6:127556/144‑1 (MQ=255)                                                          ccgccgGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCCCTGCCCCAGGCCTTGGCC‑‑AGGGGTCGGACCATGTGCAGGGGCTGTGCGCGCGGGCCAGCCCGCGAATGGGCCCCGcgc                                                                                            >  6:94908/1‑146 (MQ=37)                                                              cgGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGACCTGCAC‑‑AAGGTCCGAACCCTGTGCAATGCCtgtggg                                                                                                                          <  6:29798/114‑3 (MQ=14)                                                              cgGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGACCTGCAC‑‑AAGGTCCGAACCCTGTGCAATGCCtgtggg                                                                                                                          >  5:29798/1‑112 (MQ=14)                                                                           ggCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCCCAGGCATTGCAC‑‑CGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAAc                                                                          <  5:227354/149‑1 (MQ=255)                                                                             cacaCCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCtg                                                                                                                              >  3:243960/1‑95 (MQ=255)                                                                             cacaCCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCtg                                                                                                                              <  4:243960/95‑1 (MQ=255)                                                                               cacCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCtt                                                                                                                                          >  3:78338/1‑81 (MQ=255)                                                                                     a‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCCCAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCg                                                                >  6:250568/1‑149 (MQ=255)                                                                                                 gCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCa                                                    <  3:108750/149‑1 (MQ=255)                                                                                                  ccGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACCGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCg                                                                                  <  1:184714/119‑1 (MQ=255)                                                                                                  ccGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCg                                                                                  >  2:184714/1‑119 (MQ=255)                                                                                                          cGGCCCATGCGCGGGCTTGCCCGCTCCCAAAGGCATTGCAC‑‑AGGTTTCGGACCTTGTGCAGTTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCa                                            <  5:220229/148‑1 (MQ=255)                                                                                                            gCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACCTCTGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAg                                           <  1:89890/149‑1 (MQ=38)                                                                                                                              ccGCTCCCACAGCCATTGCAC‑‑CGGGTTCGCACCTTGTCCAGGTCCTTGGCGAGCGGCAAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTc                       <  3:136544/149‑1 (MQ=255)                                                                                                                                    ccACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCCAAGGTCAGTTATTCAGGCATCACACACATGGTGTTCGTTGa                  >  7:104725/1‑149 (MQ=255)                                                                                                                                    ccACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTgg                            <  2:256261/138‑1 (MQ=255)                                                                                                                                    ccACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTgg                            >  1:256261/1‑138 (MQ=255)                                                                                                                                    ccACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTgcc                 >  7:199204/1‑147 (MQ=255)                                                                                                                                         ggCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTgaga            <  5:250568/149‑1 (MQ=255)                                                                                                                                         ggCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTgaga            <  1:186001/149‑1 (MQ=255)                                                                                                                                          gCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGagag           >  1:171936/1‑149 (MQ=255)                                                                                                                                                cac‑‑aGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCg     >  3:66260/1‑149 (MQ=255)                                                                                                                                                 ac‑‑aGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGt    >  5:76590/1‑149 (MQ=255)                                                                                                                                                     aGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTc  <  6:76590/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                     TGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAA‑GTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCAC‑‑AGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCG‑CCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTC  >  NC_002947/2063055‑2063348

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: ‑