Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,048,590	A→G	8.7%	intergenic (+45/‑251)	PP_2661 → / → PP_2662	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,048,590	0	A	G	8.7%	158.5 / 4.4	57	intergenic (+45/‑251)	PP_2661/PP_2662	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (23/29);  new base G (2/3);  total (25/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGACGCGGTGGTGGATGTGCAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGACCAAATCACCGGGCCGTACCCT  >  NC_002947/3048449‑3048737                                                                                                                                                |                                                                                                                                                    ggACGCGGTGGTGGATGTGCAGGCACAGGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCtt                                                                                                                                               >  1:197283/1‑149 (MQ=255) ggACGCGGTGGTGGATGTGCAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATTCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTc                                                                                                                                              <  2:127526/149‑1 (MQ=255)   aCGCGGTGGTGGATGTGCAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCAAAGCAGccccaatt                                                                                                                                            <  1:118869/149‑6 (MQ=255)       ggtggtGGATGTGCAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGc                                                                                                                                        <  1:371994/149‑1 (MQ=255)       ggtggtGGATGTGCAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGc                                                                                                                                        <  1:303754/149‑1 (MQ=255)       ggtggtGGATGTGCAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGc                                                                                                                                        >  5:99022/1‑149 (MQ=255)          ggtggATGTGCAGGCGC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCCGCCTTGCGGCCCTTCGCGGGctcg                                                                                                                                     >  4:107258/1‑146 (MQ=255)                tgtgCAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAACGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGc                                                                                                                                        <  8:39550/140‑1 (MQ=255)                tgtgCAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAAAGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGc                                                                                                                                        >  7:39550/1‑140 (MQ=255)                  tgCAGGCGC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCCGCCTTGCGGCCCTTCGCGGGCTCGCCCGCGaa                                                                                                                             <  3:107258/149‑1 (MQ=39)                  tgCAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGTCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGCGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGaa                                                                                                                             <  4:88830/149‑1 (MQ=255)                    cAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCCTGCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCTCGCCCGCGAAg                                                                                                                            <  1:294624/149‑1 (MQ=255)                    cAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCCGCCTTGCGGCCCTTCGCGGGCTCGCCCGCGAAg                                                                                                                            <  2:140548/148‑1 (MQ=39)                       gCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGTCACTGGCTTCATGAAGACAGGAGATTCC‑GCTCAGATAATGTAATTGGGTCTGCTTTGCAGCCCTTCGCGGGAGAGCACGCGAAGGGcc                                                                                                                        >  2:363008/1‑149 (MQ=255)                                   ctggcAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTcgc                                                                                                                                            >  7:178830/1‑118 (MQ=255)                                   ctggcAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTcgc                                                                                                                                            <  8:178830/118‑1 (MQ=255)                                   ctggcAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCCGCCTTGCGGCCCTTCGCGGGCTCGCCCGCGAAGGGCTGCAAagc                                                                                                                 >  3:253849/1‑145 (MQ=37)                                   ctggcAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCCGCCTTGCGGCCCTTCGCGGGCTCGCCCGCGAAGGGCTGCAAagc                                                                                                                 <  4:253849/145‑1 (MQ=37)                                        agcaACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCTCGCCCGCGAAGGGCCGCAAGGCGGCCCCGGt                                                                                                        >  4:288689/1‑149 (MQ=255)                                         gcaACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAggcggc                                                                                                              <  5:81143/142‑1 (MQ=255)                                         gcaACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAggcggc                                                                                                              >  6:81143/1‑142 (MQ=255)                                         gcaACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGtt                                                                                                       >  7:211345/1‑149 (MQ=255)                                          caACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttc                                                                                                      <  8:341915/149‑1 (MQ=255)                                             ccGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttcatt                                                                                                   <  2:197283/149‑1 (MQ=255)                                               gCACCGTTATGAAATGCCCGCTTGCCAGCGGTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttcattca                                                                                                 <  5:344254/149‑1 (MQ=255)                                                         gAAATGCCTGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGa                                                                                                                                      <  7:273386/102‑1 (MQ=255)                                                         gAAATGCCTGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGa                                                                                                                                      >  8:273386/1‑102 (MQ=255)                                                                ccGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGc                                                                                <  8:211345/149‑1 (MQ=255)                                                                 cGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGcc                                                                               >  6:44086/1‑149 (MQ=255)                                                                 cGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGc                                                                                >  4:30292/1‑148 (MQ=255)                                                                      gCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGTAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGcc                                                                           <  8:361011/148‑1 (MQ=255)                                                                      gCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttca                                                                                                     >  6:177577/1‑122 (MQ=255)                                                                      gCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttca                                                                                                     <  5:177577/122‑1 (MQ=255)                                                                      gCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGc                                                                            <  6:99022/147‑1 (MQ=255)                                                                          gCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTcc                                                                      >  8:242514/1‑149 (MQ=255)                                                                            gTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTcctg                                                                    <  5:44086/149‑1 (MQ=255)                                                                                    gCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGTCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGc                                                             >  3:330486/1‑148 (MQ=255)                                                                                          gCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTcctgc                                                                   >  8:63736/1‑136 (MQ=255)                                                                                          gCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATACAATCGTATTGATACCCGCCTGCCACTcctgc                                                                   <  7:63736/136‑1 (MQ=255)                                                                                              ccTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGTCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGtct                                                    <  4:330486/147‑1 (MQ=255)                                                                                                 gAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGc                                                                                >  1:225470/1‑116 (MQ=255)                                                                                                 gAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGc                                                                                <  2:225470/116‑1 (MQ=255)                                                                                                 gAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTcct                                                                     >  1:145063/1‑127 (MQ=255)                                                                                                 gAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTcct                                                                     <  2:145063/127‑1 (MQ=255)                                                                                                      cAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGa                                                               <  5:304054/128‑1 (MQ=255)                                                                                                      cAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGa                                                               >  6:304054/1‑128 (MQ=255)                                                                                                       aGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGAc                                         >  6:154068/1‑149 (MQ=255)                                                                                                        ggAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttcat                                                                                                    <  2:311237/89‑1 (MQ=255)                                                                                                        ggAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttcaa                                                                                                    >  1:311237/1‑88 (MQ=255)                                                                                                               cc‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCa                                  <  7:242514/148‑1 (MQ=255)                                                                                                                    tCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCaa                                                                                                <  1:135223/82‑1 (MQ=255)                                                                                                                    tCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCaa                                                                                                >  2:135223/1‑82 (MQ=255)                                                                                                                      aGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTAc                             <  5:154068/147‑1 (MQ=255)                                                                                                                         tAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCTCGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGa                        <  3:288689/149‑1 (MQ=255)                                                                                                                          aaTGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGAc                       >  7:59364/1‑149 (MQ=255)                                                                                                                               aaTTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGACCaaa                   >  1:265150/1‑148 (MQ=255)                                                                                                                                               cAGCCATTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCAGCCACTCCTGCCTGAGCCATAAGTCTCG‑ACCAGGACCCAAGCAGGTACCGTGACCAAATCACCGGGCCGTACCCt  <  3:30292/148‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                    GGACGCGGTGGTGGATGTGCAGGCAC‑GGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGACCAAATCACCGGGCCGTACCCT  >  NC_002947/3048449‑3048737

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: ‑