Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,719,284	C→A	7.4%	intergenic (+45/+85)	PP_1514 → / ← PP_1515	hypothetical protein/Transcriptional regulator, tetR family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,719,284	0	C	A	7.4%	166.0 / 4.2	54	intergenic (+45/+85)	PP_1514/PP_1515	hypothetical protein/Transcriptional regulator, tetR family
Reads supporting (aligned to +/- strand):  ref base C (23/27);  new base A (2/2);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.25e-01

TTGGATGCGGTTAATGCTCGTATGTCCGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGTAAGAACACTTTTACCACCTCGCGCACATGTGCCTCGGCTT  >  NC_002947/1719141‑1719427                                                                                                                                                |                                                                                                                                                 ttGGATGCGGTTAATTCTCGTATGTCCGCATCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTc                                                                                                                                              <  6:262653/148‑1 (MQ=255)   ggATGCGGTTAATGCTCGTATGTCCGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCAc                                                                                                                                            <  4:84084/148‑1 (MQ=255)        cGGTTAATGCTCGTATGTCCGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaa                                                                                                                                      <  1:302847/149‑1 (MQ=255)          gTTAATGCTCGTATGTCCGCAGCGGGATCCTCGCGAGACCAAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTTGGTGTGATGAACTCTATATCAGCTACCTTCTACGTGAGTGCACGCagaagg                                                                                                                                    <  6:180019/149‑1 (MQ=255)             aaTGCTCGTATGTCCGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTa                                                                                                                                         >  2:41262/1‑141 (MQ=255)             aaTGCTCGTATGTCCGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTa                                                                                                                                         <  1:41262/141‑1 (MQ=255)               tGCTCGTATGTCCGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaaggcag                                                                                                                                 >  3:347541/1‑147 (MQ=255)                gCTCGTATGTCCGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTACGTGAGTGCACGCagaaggtagct                                                                                                                               >  6:175794/1‑146 (MQ=255)                     tATGTCCGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTACGTGAGTGCACGCagaaggt                                                                                                                                   <  5:140275/139‑2 (MQ=255)                     tATGTCCGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTACGTGAGTGCACGCagaaggt                                                                                                                                   >  6:140275/1‑138 (MQ=255)                      aTGTCCGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaaggcagaatgaag                                                                                                                          >  8:239722/1‑142 (MQ=255)                         tCCGCAGCGGGATCCGCTCGAGACATAATGATTAAAGCCGAGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATTAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaaggcagaaggcagaa‑ggc                                                                                                                    <  8:204942/149‑1 (MQ=255)                           cGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaaggcagaaggcagaa‑gg                                                                                                                     >  6:127721/1‑146 (MQ=255)                             cAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaa                                                                                                                                      >  2:26721/1‑128 (MQ=255)                             cAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaa                                                                                                                                      <  1:26721/128‑1 (MQ=255)                                cGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaaggcagaaggcagaa‑ggcagaaggc                                                                                                             <  4:347541/149‑1 (MQ=255)                                  ggATCCTCGCGAGACCTAATCATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGaaggcagaaggcagaa‑ggcagaaggcag                                                                                                           <  3:290244/149‑1 (MQ=255)                                                 cTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAggcagaaggcagaa‑ggcagaaggcagaa                                                                                                         <  8:164056/136‑1 (MQ=255)                                                 cTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAggcagaaggcagaa‑ggcagaaggcagaa                                                                                                         >  7:164056/1‑136 (MQ=255)                                                    aTGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGc                                                                                          <  6:207159/148‑1 (MQ=255)                                                     tGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGa                                                                                        <  5:35305/149‑1 (MQ=255)                                                       aTTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGAtt                                                                                      <  8:236532/149‑1 (MQ=255)                                                       aTTCAAGACGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGAt                                                                                       <  6:268256/148‑1 (MQ=255)                                                           aaGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGaa                                                                                   >  5:117443/1‑148 (MQ=255)                                                                  gTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTAtt                                                                           <  5:127721/149‑1 (MQ=255)                                                                      aTAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTaa                                                                         >  5:34546/1‑147 (MQ=255)                                                                      aTAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTaa                                                                         <  6:34546/147‑1 (MQ=255)                                                                             agaTCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaaggcagaaggcagaa‑ggcagaaggc                                                                                                             >  2:164378/1‑104 (MQ=255)                                                                             agaTCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaaggcagaaggcagaa‑ggcagaaggc                                                                                                             <  1:164378/104‑1 (MQ=255)                                                                                  aGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaaggcagaaggcagaa‑g                                                                                                                      <  7:9298/90‑1 (MQ=255)                                                                                  aGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaaggcagaaggcagaa‑g                                                                                                                      >  8:9298/1‑90 (MQ=255)                                                                                    aaGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaaggc                                                                                                                                   >  4:148520/1‑76 (MQ=255)                                                                                    aaGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTagaaggc                                                                                                                                   <  3:148520/76‑1 (MQ=255)                                                                                    aaGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGa                                                                                        >  4:83164/1‑118 (MQ=255)                                                                                            ccGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTaa                                                                         <  1:287323/125‑1 (MQ=255)                                                                                            ccGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTaa                                                                         >  2:287323/1‑125 (MQ=255)                                                                                                 tAAAAGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGccc                                            <  8:141671/149‑1 (MQ=255)                                                                                                   aaTGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTtc                                                             >  6:223300/1‑130 (MQ=255)                                                                                                   aaTGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTtc                                                             <  5:223300/130‑1 (MQ=255)                                                                                                    aTGGCTTGGGTGTGATGAACTCTATTTCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGt                                          >  2:226190/1‑148 (MQ=255)                                                                                                     tGGCTTGTGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCAAGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGTaa                                        <  7:239722/149‑1 (MQ=255)                                                                                                                tgattaAATCTATATCATCTACCTTCTGCTTTCACTCAAGTATAATGCAGAAGGCAGAA‑GGCAGAAGGCATAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGTAAGAACACtttt                              <  5:349971/148‑1 (MQ=255)                                                                                                                tgatgaACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGTAAGAACACTTTTa                             >  2:290363/1‑149 (MQ=255)                                                                                                                       ctctATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGTAAGAACACTTTTACAACCTc                      >  4:119043/1‑149 (MQ=255)                                                                                                                          tattTCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGTAAGAACACTTTTACCACCTcg                     <  1:226190/147‑1 (MQ=255)                                                                                                                                aGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTaaa                                                 >  6:214217/1‑113 (MQ=255)                                                                                                                                aGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTaaa                                                 <  5:214217/113‑1 (MQ=255)                                                                                                                                      cTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGTAAGAACACTTTTACCACCTCGCGCACATGTGcc         >  2:307897/1‑147 (MQ=255)                                                                                                                                      cTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGTAAGAACACTTTTACCACCTCGCGCACATGTGcc         <  1:307897/147‑1 (MQ=255)                                                                                                                                           gCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGTAAGAACACTTTTACCACCTCGCGCACATGTGCCTCGGCt   >  7:1750/1‑148 (MQ=255)                                                                                                                                            cGTGCACTCACGTAGAAGGCAGAAGGCAGAAGGGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTcc                                                      >  1:42582/1‑97 (MQ=255)                                                                                                                                            cGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GTGAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTcc                                                      <  2:42582/96‑1 (MQ=255)                                                                                                                                            cGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGTAAGAACACTTTTACCACCTCGCGCACATGTGCCTCGGCtt  >  2:175344/1‑148 (MQ=255)                                                                                                                                             gTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGt                                          >  2:272715/1‑107 (MQ=255)                                                                                                                                                |                                                                                                                                                 TTGGATGCGGTTAATGCTCGTATGTCCGCAGCGGGATCCTCGCGAGACCTAATGATTCAAGCCGCGTTAATAGCAGAGATCAGAAGGCGTCCCGCATAAATGGCTTGGGTGTGATGAACTCTATATCAGCTACCTTCTGCGTGCACTCACGTAGAAGGCAGAAGGCAGAA‑GGCAGAAGGCAGAAGTTTGGCTAGTGAGCGATTGAAAAAGTATTAATGAAGATTTTTCTCAGTCCCTAAACGCCCGTAAGAACACTTTTACCACCTCGCGCACATGTGCCTCGGCTT  >  NC_002947/1719141‑1719427

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: ‑