Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,765,972	A→T	8.5%	intergenic (+15/‑32)	PP_1576 → / → PP_1577	immunity protein/lambda family tail tape meausure protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,765,972	0	A	T	8.5%	144.0 / 5.0	54	intergenic (+15/‑32)	PP_1576/PP_1577	immunity protein/lambda family tail tape meausure protein
Reads supporting (aligned to +/- strand):  ref base A (18/29);  new base T (2/2);  total (22/32)
Fisher's exact test for biased strand distribution p-value = 6.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.20e-01

TTCCAGTTGGTCAGATTGAGAGAGTCGGCAGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGAGCGCAGCTCAGAAAAGTGGCGAAAGCAGGTC  >  NC_002947/1765824‑1766117                                                                                                                                                      |                                                                                                                                                  ttccagttGGTCAGATTGAGAGAGTCGGCAGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑Caa                                                                                                                                                  <  2:1073835/150‑1 (MQ=255)   gcagttGGTCAGATGGAGAGAGGCGGCAGTGCGTCTAGGGATGAAGAGCTTGAGAAAATGTGGGCCCGCCGAAGCAGCGGAGCTTTAACTGCGGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGt                                                                                                                                                <  2:1080244/149‑1 (MQ=255)    cAGTTGGTCAGATTGAGAGAGTCGGCAGTTCGTCTAGGTATGAAGAGATTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTg                                                                                                                                               <  1:820741‑M2/150‑2 (MQ=255)      gTTGGTCAGATTGAGAGAGTCGGCAGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTgcg                                                                                                                                             <  1:1196350‑M2/150‑4 (MQ=255)          gTCAGATTGAGAGAGTCGGCAGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTgcgggtt                                                                                                                                         <  2:527484‑M2/150‑8 (MQ=255)          gTCAGATTGAGAGAGTCGGCAGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTgcgggtt                                                                                                                                         <  1:309119‑M2/150‑8 (MQ=255)              gATTGAGAGAGTCGGCAGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGtttttt                                                                                                                                     <  1:601856/150‑1 (MQ=255)                   agagagTCGGCAGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑ACTTGgcgggtttttatttca                                                                                                                                >  1:1007109‑M2/1‑134 (MQ=255)                      gagTCGGCAGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCg                                                                                                                             <  2:820741/150‑1 (MQ=255)                         tCGGCAGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGGAATTCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAAACCAC‑ACTTGgcggggttttatttcactttag                                                                                                                          <  1:1114730‑M2/150‑23 (MQ=255)                            gCAGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGaaa                                                                                                                       <  1:193056/150‑1 (MQ=255)                              aGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAAc                                                                                                                     >  2:877097/1‑150 (MQ=255)                                 tCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAAt                                                                                                                  <  2:1196350/150‑1 (MQ=255)                                   gTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGga                                                                                                                           >  1:213653/1‑139 (MQ=255)                                   gTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGga                                                                                                                           <  2:213653/139‑1 (MQ=255)                                    tCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTACATGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGc                                                                                                               <  1:317796/150‑1 (MQ=255)                                    tCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGc                                                                                                               <  2:726064/150‑1 (MQ=255)                                         gTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCaa                                                                                                          <  2:219940/150‑1 (MQ=255)                                           aTGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGCACTTGcgggtttttatttcactttagtattcga                                                                                                                     >  1:284175‑M2/1‑111 (MQ=255)                                           aTGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGCACTTGcgggtttttatttcactttagtattcga                                                                                                                     <  2:284175‑M2/139‑29 (MQ=255)                                            tGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACaa                                                                                                                   >  2:1073759/1‑138 (MQ=255)                                            tGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACaa                                                                                                                   <  1:1073759/138‑1 (MQ=255)                                            tGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGAt                                                                                                       <  1:243422/150‑1 (MQ=255)                                             gAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑ACTTGgcgggtttttatttcactttagtattcgagacttctcccgat                                                                                                      >  2:1114730‑M2/1‑108 (MQ=255)                                                         aaaaTTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCActct                                                                                          <  2:309119/150‑1 (MQ=255)                                                             tttCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGCACTTGcgggtttttatttcactttagtattcga                                                                                                                     >  2:892268‑M2/1‑93 (MQ=255)                                                             tttCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGCACTTGcgggtttttatttcactttagtattcga                                                                                                                     <  1:892268‑M2/121‑29 (MQ=255)                                                             tttCGGCCCTCCGAAGCAGCGG‑GCTTTAACTGCCGAGGAGCTCGACCGGGACTAGTCTTGAATAATAAAGGGAAATAAAAACCCGC‑CAAGTGCGGGGTTTTTAATGTCCGGGGAAAAAAACTGTGGCAAGATCTCTCGGCACTCTGAccc                                                                                     >  1:813443/1‑150 (MQ=255)                                                               tCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCt                                                                                    <  1:498950/150‑1 (MQ=255)                                                                 ggCCCTCCGAAGCAGCGGAGCTTTAACTGGCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTg                                                                                  <  1:877097/150‑1 (MQ=255)                                                                         gAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATa                                                                          >  1:193925/1‑150 (MQ=255)                                                                                      tttAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTGTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCg                                                             >  2:834503/1‑150 (MQ=255)                                                                                         aaCTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGtt                                                          >  1:313948/1‑150 (MQ=255)                                                                                            tGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCg                                                       >  1:282849/1‑150 (MQ=255)                                                                                                 aggagTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGcc                                                  <  2:21728/150‑1 (MQ=255)                                                                                                      ttCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCAt                                             >  1:724556/1‑150 (MQ=255)                                                                                                      ttCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCAt                                             <  2:282849/150‑1 (MQ=255)                                                                                                                  aaGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGa                                 <  1:764629/150‑1 (MQ=255)                                                                                                                   aGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGAg                                <  1:751952/150‑1 (MQ=255)                                                                                                                     tctcGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGAgcg                              >  2:65609/1‑150 (MQ=255)                                                                                                                            tACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGAGCGCAGCTCa                       <  1:527484/150‑1 (MQ=255)                                                                                                                              cTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGa                                                                                        >  2:1004759/1‑83 (MQ=255)                                                                                                                              cTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGa                                                                                        <  1:1004759/83‑1 (MQ=255)                                                                                                                               tAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGAGCGCAGCTCAGaa                    >  2:782632/1‑150 (MQ=255)                                                                                                                                aaaGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGAGCGCAGCTCAGaaa                   >  1:1032353/1‑150 (MQ=255)                                                                                                                                 aaGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCgg                                                                                                <  1:754787/72‑1 (MQ=255)                                                                                                                                 aaGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCgg                                                                                                >  2:754787/1‑72 (MQ=255)                                                                                                                                    tGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGAt                                                                                >  2:492303/1‑85 (MQ=255)                                                                                                                                    tGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGAt                                                                                <  1:492303/85‑1 (MQ=255)                                                                                                                                    tGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGAGCGCAGCTCAGAAAAGTg               >  2:287852/1‑150 (MQ=255)                                                                                                                                     gAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGAGCGCAGCTCAGAAAAGTgg              <  2:724556/150‑1 (MQ=255)                                                                                                                                      aaaTAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGAt                                                                                >  2:92409/1‑83 (MQ=255)                                                                                                                                      aaaTAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGAt                                                                                <  1:92409/83‑1 (MQ=255)                                                                                                                                      aaaTAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGAGCGCAGCTCAGAAAAGTGGc             <  1:65609/150‑1 (MQ=255)                                                                                                                                                 cGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGAGCGCAGCTCAGAAAAGTGGCGAAAGCAGGTc  >  1:663772/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                  TTCCAGTTGGTCAGATTGAGAGAGTCGGCAGTTCGTCTAGGTATGAAGAGCTTGAGAAAATTTCGGCCCTCCGAAGCAGCGGAGCTTTAACTGCCGAGGAGTTCGATCGGGAGAAGTCTCGAATACTAAAGTGAAATAAAAACCCGC‑CAAGTGCGGGTTTTTTAATGTCCGGAGAAAACAATGGCGTCAAGATCTCTCGGCACTCTGACCCTTGATGTCATAGCCCAGGTAGGCGGTTTCGTTGCCGGCATGGATAAGGCCGAGCGCAGCTCAGAAAAGTGGCGAAAGCAGGTC  >  NC_002947/1765824‑1766117

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑