Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,604,693	A→C	7.3%	intergenic (‑40/‑88)	PP_3179 ← / → PP_3180	LysR family transcriptional regulator/Smp‑30/Cgr1 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,604,693	0	A	C	7.3%	164.3 / 3.7	55	intergenic (‑40/‑88)	PP_3179/PP_3180	LysR family transcriptional regulator/Smp‑30/Cgr1 family protein
Reads supporting (aligned to +/- strand):  ref base A (21/30);  new base C (2/2);  total (23/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.02e-01

GCCTGGCTCAGCGGCGGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATCCCACTGATTGCACCTTGCGC  >  NC_002947/3604547‑3604837                                                                                                                                                   |                                                                                                                                                 gCCTGGCTCAGCGGCGGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATg                                                                                                                                                >  4:309873/1‑149 (MQ=255) gCCTGGCTCAGCGGCGGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATg                                                                                                                                                >  2:126909/1‑149 (MQ=255)  ccTGGCTCAGCGGCGGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATgg                                                                                                                                               <  4:117140/149‑1 (MQ=255)           gcggcgGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCCATGGATATCacc                                                                                                                                      <  1:164860/149‑3 (MQ=255)                 gTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCa                                                                                                                                <  8:226825/149‑1 (MQ=255)                      gcCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCtt                                                                                                                           >  3:62028/1‑149 (MQ=255)                       ccATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGACCAAGCGTGATTCGATCATCCAGCATTCCTCCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCatt                                                                                                                          >  6:163510/1‑149 (MQ=255)                          tgtgCAGGCTCTGTGCGTCCTTGTGAAAGTTCAGCTCTTCTGCCACGGCGATGAACTGCCTGATCAAGCGTGTTTCTATCATCCAGCATTCCTGCATCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTaa                                                                                                                       <  6:82275/149‑1 (MQ=255)                            tgCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAat                                                                                                                      <  7:218278/148‑1 (MQ=255)                             gCAGGCGCTGTGCGGCCTTGTGAAAGTGAAGCTCATCGGCCACGGCGATGAACTGCATGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGAGACTCGGCGGTGATATCCATTGGATATCAAAGTTGCATGCTTTTAatat                                                                                                                    >  5:257696/1‑149 (MQ=255)                              cAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATAtt                                                                                                                   <  8:268385/149‑1 (MQ=255)                                ggCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTaa                                                                                                                 <  3:277415/149‑1 (MQ=255)                                 gcgcTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAg                                                                                                                >  6:248414/1‑149 (MQ=255)                                          ggCCTTGTGTAAGTGCAGCTCTTGGTCCACGGCGATGAAGTGCGTTAGCAAGCGTGTTTCGATCATCGAGCATTGCTGGAGCGTGGCGAGTCGGCGGTGATATCCATGTGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGAtt                                                                                                       <  4:129925/149‑1 (MQ=255)                                          ggCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGAtt                                                                                                       <  6:105570/149‑1 (MQ=255)                                           gCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTaa                                                                                                                       <  5:215787/132‑1 (MQ=255)                                           gCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTaa                                                                                                                       >  6:215787/1‑132 (MQ=255)                                                gtgAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGAttttttt                                                                                                  <  5:248414/148‑1 (MQ=255)                                                gtgAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGAttttttt                                                                                                  <  3:108840/148‑1 (MQ=255)                                                gtgAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTttg                                                                                                 >  2:48103/1‑149 (MQ=255)                                                   aaaGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTttgttg                                                                                              <  3:234569/149‑1 (MQ=255)                                                      gTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGata                                                                                           <  5:305704/149‑1 (MQ=255)                                                         cAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCg                                                                                        >  3:223595/1‑149 (MQ=255)                                                         cAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCg                                                                                        >  5:221964/1‑149 (MQ=255)                                                         cAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCg                                                                                        >  6:202143/1‑149 (MQ=255)                                                          aGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCg                                                                                        >  4:303431/1‑148 (MQ=255)                                                            ctctTCGGCCTCGGCGATGAACTGCCTGAGCAAGCGTTGTTCGATCATACAGCATTCCTGCAGGGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGTTATCGTaa                                                                                     <  4:223595/149‑1 (MQ=255)                                                            ctctTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGt                                                                                       >  6:119877/1‑147 (MQ=255)                                                            ctctTCGGCCAAGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTaa                                                                                     <  6:221964/149‑1 (MQ=255)                                                                 cGGCCACGGCGATGTACTGCCTGAGCAAGCGTGTTTCTATGTTCCAGCTTTCCTTCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCATTGTTGCATGCTTTTAATATTAAGTCTTTGTTTTTTTTGTTGATATCGTAAGaaa                                                                                 <  5:163510/148‑1 (MQ=255)                                                                   gCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGga                                                                              <  4:62028/149‑1 (MQ=255)                                                                           gATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGaa                                                                      <  1:126909/149‑1 (MQ=255)                                                                           gATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGaa                                                                      <  1:48103/149‑1 (MQ=255)                                                                           gATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGaa                                                                      <  3:309873/149‑1 (MQ=255)                                                                               aaCTGACTGAGCAAGCGTGTTTCGATAATCCAGCATTCATGCAGCGTGGCGACTCGGCGTTGATATACATGGGATATAAAAGTTGCATGCTTATAATATTAAGTCATTTATTTTTTTGTTGATATCGTAAGAAAGTAGAATTGAAgg                                                                    >  8:47741/1‑147 (MQ=255)                                                                                aCTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTa                                                                  <  5:119877/148‑1 (MQ=255)                                                                                aCTGACTTAGCAAGAGTGTTTCTTTCATCCAGCATTCCTGAAGCGTTGCGACTCTGCGGTTATATAAATGTGATATCAAAGTTGCATGCTTTTAATATTAAGTAATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTa                                                                  <  7:47741/148‑1 (MQ=255)                                                                                    ccTGAGCAAGCGTGTTTCGATCATCGAGCATTGCTGCAGCGGGGCTACTCGGGGGTTATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCTTAAGAAAGGAGAATTGAAGGTAGCCa                                                              <  6:257696/148‑1 (MQ=255)                                                                                                  tttCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACt                                               >  5:14273/1‑149 (MQ=255)                                                                                                             cAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCg                                     <  5:202143/148‑1 (MQ=255)                                                                                                             cAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCg                                     <  6:14273/148‑1 (MQ=255)                                                                                                              aGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGaa                                                                           <  8:185577/109‑1 (MQ=255)                                                                                                              aGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGaa                                                                           >  7:185577/1‑109 (MQ=255)                                                                                                              aGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGt                                   >  2:252869/1‑149 (MQ=255)                                                                                                                                 gACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAg                                                                                >  4:50777/1‑85 (MQ=255)                                                                                                                                 gACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAg                                                                                <  3:50777/85‑1 (MQ=255)                                                                                                                                  aCTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATCCAACTGa               >  2:202655/1‑149 (MQ=255)                                                                                                                                   cTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATCCCACTGAt              <  1:252869/149‑1 (MQ=255)                                                                                                                                      aactttGATATCCCATGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATCCCACTGATTg            >  1:11805/6‑148 (MQ=255)                                                                                                                                         tttGATATCCCATGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATc                      >  6:259730/3‑135 (MQ=255)                                                                                                                                         tttGATATCCCATGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATc                      <  5:259730/133‑1 (MQ=255)                                                                                                                                             atatCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATCCCACTGATTGCACCTTgc    >  6:239823/1‑149 (MQ=255)                                                                                                                                               atCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCa                                             <  3:125760/106‑1 (MQ=255)                                                                                                                                               atCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCa                                             >  4:125760/1‑106 (MQ=255)                                                                                                                                                tCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATCCCACTGATTGCACCTTgcgc  <  3:303431/148‑1 (MQ=255)                                                                                                                                                   aTGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTGCTCACCTGGCCGGTGCGCTGTGCCATCCCACTGATTGCACCtt      >  6:154151/1‑141 (MQ=255)                                                                                                                                                   aTGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTGCTCACCTGGCCGGTGCGCTGTGCCATCCCACTGATTGCACCtt      <  5:154151/141‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                 GCCTGGCTCAGCGGCGGTTGCGCCATGTGCAGGCGCTGTGCGGCCTTGTGAAAGTGCAGCTCTTCGGCCACGGCGATGAACTGCCTGAGCAAGCGTGTTTCGATCATCCAGCATTCCTGCAGCGTGGCGACTCGGCGGTGATATCCATGGGATATCAAAGTTGCATGCTTTTAATATTAAGTCATTGATTTTTTTGTTGATATCGTAAGAAAGGAGAATTGAAGGTAGCCAGAAATGCCCGTTACTCACCTGGCCGGTGCGCTGTGCCATCCCACTGATTGCACCTTGCGC  >  NC_002947/3604547‑3604837

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑