Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,475,092	C→G	7.5%	P148P (CCG→CCC)	PP_3964 ←	transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,475,092	0	C	G	7.5%	158.2 / 3.8	53	P148P (CCG→CCC)	PP_3964	transposase
Reads supporting (aligned to +/- strand):  ref base C (26/23);  new base G (2/2);  total (28/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.35e-01

GGCCACCATCACGTGGGCCAACAAACCTGTGGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGTTTCGGGGATTGTCGTGGT  >  NC_002947/4474951‑4475239                                                                                                                                                |                                                                                                                                                      ggCCACCATCACGTGGGCCAACAAACCTGTGGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCgt                                                                                                                                                  <  8:127548/147‑1 (MQ=255)    caccaTCACGTGGGCCAACAAACCTGTGGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCGGGCgtgttta                                                                                                                                             <  5:79361/149‑4 (MQ=255)    caccaTCACGTGGGCCAACAAACCTGTGGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAAt                                                                                                                                             >  5:295959/1‑149 (MQ=255)       caTCACGTGGGCCAACAAACCTGTGGTCGGGATACCTTTGTCGATTACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATc                                                                                                                                            >  1:222386/1‑147 (MQ=255)       caTCACGTGGGCCAACAAACCTGTGGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATc                                                                                                                                            >  7:74484/1‑147 (MQ=255)             gTGGGCCAACAAACCTGTGGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTtct                                                                                                                                    >  5:201906/1‑149 (MQ=255)               gggCCAACAAACCTGTGGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCg                                                                                                                                  <  6:201906/149‑1 (MQ=255)                ggCCAACAAACCTGTGGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGc                                                                                                                                 >  2:290497/1‑149 (MQ=255)                       aaaCCTGTGGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACGGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTc                                                                                                                          >  4:90139/1‑149 (MQ=255)                          ccTGTGGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTc                                                                                                                       <  1:290497/149‑1 (MQ=255)                              tgGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGc                                                                                                                     <  1:46472/147‑1 (MQ=255)                                 tCGGGATACCTTTGTCGATAACCTGGGCTGGGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTg                                                                                                                               >  1:189002/1‑135 (MQ=255)                                 tCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTg                                                                                                                               <  2:189002/134‑1 (MQ=255)                                          cTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGGACCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAg                                                                                                      >  1:91062/1‑149 (MQ=255)                                            ttGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGaa                                                                                                       >  8:79078/1‑145 (MQ=255)                                            ttGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGaa                                                                                                       <  7:79078/145‑1 (MQ=255)                                             tGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTg                                                                                                   <  2:222386/148‑1 (MQ=255)                                                 gATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGc                                                                                              >  5:106057/1‑149 (MQ=255)                                                     aCCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGaa                                                                                                       >  6:283866/1‑136 (MQ=255)                                                     aCCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGaa                                                                                                       <  5:283866/136‑1 (MQ=255)                                                       cTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGc                                                                                                              >  2:174875/1‑128 (MQ=255)                                                       cTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGc                                                                                                              <  1:174875/128‑1 (MQ=255)                                                       cTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGATAGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGACACAGa                                                                                        >  1:268877/1‑149 (MQ=255)                                                        tGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCg                                                                                                                      <  4:237928/120‑1 (MQ=255)                                                                gCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGc                                                                                                 <  4:172524/132‑1 (MQ=255)                                                                gCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGc                                                                                                 >  3:172524/1‑132 (MQ=255)                                                                         ccTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCg                                                                       <  2:91062/149‑1 (MQ=255)                                                                         ccTGGATCAGGGATTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAAGACGCCCGGAGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCAGAGACGCACTGGGTGTTTTCg                                                                       <  3:274055/149‑1 (MQ=255)                                                                          cTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCgg                                                                      <  6:295959/149‑1 (MQ=255)                                                                                                cGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCGCTTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGa                                                              <  1:228637/136‑1 (MQ=255)                                                                                                cGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGa                                                              >  2:228637/1‑135 (MQ=255)                                                                                                                     cacaTGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAg                            >  5:86841/1‑149 (MQ=40)                                                                                                                        aTGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGgcg                         >  3:119347/1‑149 (MQ=255)                                                                                                                             gCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCggcggc                                <  2:288308/137‑1 (MQ=40)                                                                                                                             gCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCggcggc                                >  1:288308/1‑137 (MQ=40)                                                                                                                               tCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTg                                       >  8:65226/1‑128 (MQ=40)                                                                                                                               tCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTg                                       <  7:65226/128‑1 (MQ=40)                                                                                                                               tCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGttt                  >  6:56071/1‑149 (MQ=255)                                                                                                                               tCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGttt                  >  6:284933/1‑149 (MQ=255)                                                                                                                                  aCGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACTCACTGGTTGTTTTCGGGTTCGTGACGAATCACCGTGAGTGGAAACTGCGGCTGCAAAGGCGCACGTTTCgg               <  2:268877/149‑1 (MQ=255)                                                                                                                                  aCGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGTTTCgg               <  8:74484/149‑1 (MQ=255)                                                                                                                                  aCGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGTTTCgg               <  6:51932/149‑1 (MQ=255)                                                                                                                                      tAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCaaa                             <  6:162110/131‑1 (MQ=40)                                                                                                                                      tAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCaaa                             >  5:162110/1‑131 (MQ=40)                                                                                                                                      tAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGTTTCGGGGAt           >  1:18235/1‑149 (MQ=255)                                                                                                                                       ttacacGCCGGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCCGGATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGTTTCgg               >  1:224090/3‑145 (MQ=255)                                                                                                                                       ttacacGCCGGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGTCGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGTTTCGGGGAtt          >  6:145928/3‑149 (MQ=255)                                                                                                                                       ttacacGCCGGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGTTTCgg               <  2:224090/142‑1 (MQ=255)                                                                                                                                          cacGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCTCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTgcggc                                   >  4:170679/1‑121 (MQ=255)                                                                                                                                          cacGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTgcggc                                   <  3:170679/121‑1 (MQ=40)                                                                                                                                          cacGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGTTTCGGGGATTGTc       >  7:245373/1‑149 (MQ=255)                                                                                                                                           acGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGTTTCGGGGATTGTCg      <  5:284933/149‑1 (MQ=255)                                                                                                                                             gCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGTTTCGGGGATTGTCGTg    >  6:252620/1‑149 (MQ=255)                                                                                                                                               ccGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTCGAAACTGCGGCGGCAAAGGCGCACGTTTCGGGGATTGTCGTGGt  >  2:308117/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                      GGCCACCATCACGTGGGCCAACAAACCTGTGGTCGGGATACCTTTGTCGATAACCTGGGCT‑GGCACCGGGGCCTGGATCAGGGTTTCGCACTGGCGACAGG‑CCCATTTGCCCCGCACATGTTGCTCGACGGTAAACACGCCCGGCGTGTAATCCAGCTTCTCGCTGACGTCTTCGCC‑GATGCG‑TTGAAGTTGGCAGCCACAGACGCACTGGGTGTTTTCGGGTTCGTGACGAATCACCGTGCGTGGAAACTGCGGCGGCAAAGGCGCACGTTTCGGGGATTGTCGTGGT  >  NC_002947/4474951‑4475239

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: ‑