Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,093,609	G→A	7.5%	R5* (CGA→TGA)	PP_4482 ←	AraC family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,093,609	0	G	A	7.5%	154.9 / 2.4	56	R5* (CGA→TGA)	PP_4482	AraC family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (26/24);  new base A (2/2);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.87e-01

CGCCAGGCGCCTTCCTGCGCAGGCTCGGCCTGCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGCTGCCGGAGAGGAACTGCTGCAGG  >  NC_002947/5093461‑5093753                                                                                                                                                      |                                                                                                                                                 cgccAGGCGCCTTCCTGCGCAGGCTCGGCCTGCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCg                                                                                                                                                  >  6:219651/1‑149 (MQ=255)       gcgcCTTCCTGCGCAGGCTCGGCCTGCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAACTGCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTggg                                                                                                                                             <  1:76347/149‑1 (MQ=255)          ccTTCCTGCGCAGGCTCGGCCTGCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGggtggt                                                                                                                                         <  2:20909/149‑1 (MQ=255)              ccTGCGCAGGCTCGGCCTGCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCAt                                                                                                                                      <  2:205323/148‑1 (MQ=255)                 gcgcAGGCTCGGCCTGCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTCGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAggg                                                                                                                                  >  7:13073/1‑149 (MQ=255)                  cgcAGGCTCGGCCTGCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAgg                                                                                                                                   <  3:35542/147‑1 (MQ=255)                     aGGCTCGGCCTGCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACg                                                                                                                              <  2:109754/149‑1 (MQ=255)                                gCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCACTGGGTGGTCATAGGGTACgg                                                                                                                             <  1:150037/139‑1 (MQ=255)                                gCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCACTGGGTGGTCATAGGGTACgg                                                                                                                             <  1:145234/139‑1 (MQ=255)                                gCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCACTGGGTGGTCATAGGGTACgg                                                                                                                             >  2:150037/1‑139 (MQ=255)                                gCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCACTGGGTGGTCATAGGGTACgg                                                                                                                             >  2:145234/1‑139 (MQ=255)                                 cAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCt                                                                                                                   <  3:153864/148‑1 (MQ=255)                                   ggAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAg                                                                                                                <  3:128101/149‑1 (MQ=255)                                            aCTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCTCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGa                                                                                                       <  8:202959/149‑1 (MQ=255)                                              tCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGt                                                                                                     >  1:47323/1‑149 (MQ=255)                                               cGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACgg                                                                                                                             >  6:264747/1‑124 (MQ=255)                                                 tAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCtg                                                                                                  >  4:73262/1‑149 (MQ=255)                                                          tCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGTGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCggg                                                                                         <  5:219651/149‑1 (MQ=255)                                                            cGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGa                                                                                                                 >  6:56660/1‑123 (MQ=255)                                                            cGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGa                                                                                                                 <  5:56660/123‑1 (MQ=255)                                                               aTGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTTGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAgg                                                                                    <  8:13073/149‑1 (MQ=255)                                                                   acacGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTgc                                                                                >  1:221680/1‑149 (MQ=255)                                                                   acacGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTgc                                                                                >  4:245851/1‑149 (MQ=255)                                                                               accaGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCcgcg                                                                      >  4:286338/1‑147 (MQ=255)                                                                                 caGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCgcag                                                                   >  6:134827/1‑148 (MQ=255)                                                                                   gCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGa                                                                                                                 <  4:97846/100‑1 (MQ=255)                                                                                    cAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCTCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATg                                                               >  4:35569/1‑149 (MQ=255)                                                                                      acacTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGcc                                                             <  2:47323/149‑1 (MQ=255)                                                                                       cacTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAg                                                                                                      >  3:94084/1‑107 (MQ=255)                                                                                       cacTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAg                                                                                                      <  4:94084/107‑1 (MQ=255)                                                                                       cacTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGccc                                                            >  2:163634/1‑149 (MQ=255)                                                                                        acTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGccc                                                            >  2:296927/1‑148 (MQ=255)                                                                                          ttCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTAt                                                         >  5:292613/1‑149 (MQ=255)                                                                                                ggCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGt                                                   <  1:296927/149‑1 (MQ=255)                                                                                                ggCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGt                                                   >  3:191980/1‑149 (MQ=255)                                                                                                  ccAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTg                                                  >  4:35705/1‑148 (MQ=255)                                                                                                    aaC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCa                                                >  7:160072/1‑148 (MQ=255)                                                                                                        gCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCaaaaa                                            <  5:293329/149‑1 (MQ=255)                                                                                                             ggTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAgg                                                                                    >  8:11521/1‑104 (MQ=255)                                                                                                             ggTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAgg                                                                                    <  7:11521/104‑1 (MQ=255)                                                                                                                  aaGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCttt                                   >  8:184439/1‑148 (MQ=255)                                                                                                                    ggCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTAc                                <  3:245851/149‑1 (MQ=255)                                                                                                                               gggCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGGACGGTCCGAAACCTGAGCTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGCTGcc                     <  3:195073/149‑1 (MQ=255)                                                                                                                                     gATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGCTGCCGGagag               >  7:2720/1‑149 (MQ=255)                                                                                                                                       tGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGCTGCCGGAGAgg              <  2:221680/148‑1 (MQ=255)                                                                                                                                        gagaAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCt                                                                                  <  7:78355/79‑1 (MQ=255)                                                                                                                                        gagaAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCt                                                                                  >  8:78355/1‑79 (MQ=255)                                                                                                                                        gagaAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTcgccgc                                                                       <  7:285297/90‑1 (MQ=255)                                                                                                                                        gagaAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTcgccgc                                                                       >  8:285297/1‑90 (MQ=255)                                                                                                                                        gagaAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGCTGCCGGAGAGGaa            >  8:165677/1‑149 (MQ=255)                                                                                                                                          gaAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGCTGCCGgag                 <  2:65002/142‑1 (MQ=255)                                                                                                                                          gaAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGCTGCCGgag                 >  1:65002/1‑142 (MQ=255)                                                                                                                                               ccGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGCTGCCGGAGAGGAAc           >  1:74132/1‑143 (MQ=255)                                                                                                                                               ccGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGCTGCCGGAGAGGAAc           <  2:74132/143‑1 (MQ=255)                                                                                                                                                 gATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGc                         >  6:280583/1‑127 (MQ=255)                                                                                                                                                 gATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGc                         <  5:280583/127‑1 (MQ=255)                                                                                                                                                  aTTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGCTGCCGGAGAGGAACTGCTGCAgg  >  7:292993/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                                 CGCCAGGCGCCTTCCTGCGCAGGCTCGGCCTGCAGGAAGACCAACTCGTAGACCACATCCGGATGCACACGCTGCGCCACCAGCAACACTTCCTCGGCCAAC‑GCCAGGGTCAAAGGCCTGGTGCTGGGCCAGATGAGAAAACCGATTCGCTGGGTGGTCATAGGGTACGGTCCGAAACCTGAGGTCGTTCGAGTCTGTGCGCCGGGTCAGGCTGCGCTCGCCGCGCAGCATGCCCTATTCTGGTGCAAAAATGCAGCTTTTACTTCAGGCTGCCGGAGAGGAACTGCTGCAGG  >  NC_002947/5093461‑5093753

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑