Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,896,414	Δ1 bp	8.5%	intergenic (+47/‑161)	PP_4304 → / → sbp‑I	VIC family cation transporter/sulfate ABC transporter substrate‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,896,414	0	G	.	8.5%	142.2 / 7.3	47	intergenic (+47/‑161)	PP_4304/sbp‑I	VIC family cation transporter/sulfate ABC transporter substrate‑binding protein
Reads supporting (aligned to +/- strand):  ref base G (18/25);  new base . (2/2);  total (20/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.05e-01

GCAGCATGATTGCCCGACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTC  >  NC_002947/4896274‑4896557                                                                                                                                             |                                                                                                                                                     gcagcaTGATTGCCCGACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑t                                                                                                                                             <  2:350372/149‑1 (MQ=255)   agcaTGATTGCCCGACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑Tgc                                                                                                                                           >  8:42407/1‑149 (MQ=255)      aTGATTGCCCGACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGcgcg                                                                                                                                        <  3:79903/149‑1 (MQ=255)         aTTGCCCGACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTc                                                                                                                                     <  1:290845/149‑1 (MQ=255)          ttGCCCGACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTcc                                                                                                                                    <  8:6525/149‑1 (MQ=255)            gCCCGACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTcc‑‑‑cc                                                                                                                               >  3:266672/1‑149 (MQ=255)                gACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCg                                                                                                                             <  8:265313/147‑1 (MQ=255)                gACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCg                                                                                                                             >  7:265313/1‑147 (MQ=255)                gACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTa                                                                                                                           <  5:59328/149‑1 (MQ=255)                gACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTa                                                                                                                           <  4:215834/149‑1 (MQ=255)                       cacaAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCgg                                                                                                                   <  7:42407/149‑1 (MQ=255)                       cacaAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCgg                                                                                                                   <  1:261079/149‑1 (MQ=255)                       cacaAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCgg                                                                                                                   <  7:121595/149‑1 (MQ=255)                           agaagaCCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGttt                                                                                                               <  4:266672/149‑1 (MQ=255)                            gaagaCCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTa                                                                                                              <  1:27519/149‑1 (MQ=255)                            gaagaCCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGACGGCCTCTTCGCGGGGAAATCCGCTCCTACATGCGCCGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTa                                                                                                              >  7:251213/1‑149 (MQ=255)                                  ccACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGG‑‑‑GGACCG‑CGCACGGTCCGCGCCTGTAGGA‑GCGGATTTAc                                                                                                             <  8:224421/144‑1 (MQ=14)                                  ccACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGG‑‑‑GGACCG‑CGCACGGTCCGCGCCTGTAGGA‑GCGGATTTAc                                                                                                             >  7:224421/1‑144 (MQ=14)                                  ccACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCgg                                                                                                                   <  2:338991/138‑1 (MQ=255)                                  ccACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCgg                                                                                                                   >  1:338991/1‑138 (MQ=255)                                       aGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGG‑‑‑GGACCG‑CGCACGGTCCGCGCCTGTAGGA‑GCGGATTTACCCGCGAagag                                                                                                   <  2:180019/149‑1 (MQ=14)                                        gCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGGGGACCG‑CGCACGGTccgcgc                                                                                                                                <  6:33750/123‑5 (MQ=38)                                        gCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGGGGACCG‑CGCACGGTccgcgc                                                                                                                                >  5:33750/1‑119 (MQ=38)                                                cggcgTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCGCCTGTAGGAGCGGatttac                                                                                                                                             <  1:234523/103‑6 (MQ=38)                                                cggcgTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCGCCTGTAGGAGCGGatttac                                                                                                                                             >  2:234523/1‑98 (MQ=38)                                                     ttctgttctCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTcc‑‑‑ccc                                                                                                                              >  1:347996/1‑109 (MQ=255)                                                     ttctgttctCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTcc‑‑‑ccc                                                                                                                              <  2:347996/109‑1 (MQ=255)                                                       ctgttctCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGa                                                                                    <  3:127042/148‑1 (MQ=255)                                                           tctcGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGAGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCa                                                                                >  5:382631/1‑148 (MQ=255)                                                             tcGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGGAGGA‑GCCGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATaa                                                                             >  5:173636/1‑149 (MQ=255)                                                                                tttCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTAGCCGGTAAATACGCTCCTAAAGGCGCGGAACG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCCGGTTTACCCGCCAAGAGGCCGGCACAAGCAGAACCATAACCAAAGCAAttttttttat                                                          >  4:298714/1‑147 (MQ=255)                                                                                    ccAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTaa                                                      >  6:108749/1‑149 (MQ=255)                                                                                               tAGCGCCTGCGCCGGCCTATTCGCTGGTAAATCCGATCCTACTGGCGCGGACCG‑TGCGCGTTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATaaa                                            <  8:251213/148‑1 (MQ=39)                                                                                                 gcgcCTGCGCCGGCCTCTTCGCGGTTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTTGTA‑GGGGTTTTACCCGCTAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAacc                                          <  1:378486/148‑1 (MQ=255)                                                                                                         gcCGGCCTCTTCGCGGGTAAATCGGCGCCTACAGGCGCGGACCG‑TGTGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTta                                 <  6:382631/149‑1 (MQ=255)                                                                                                           cGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTtata                               >  6:218569/1‑149 (MQ=255)                                                                                                                tctTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGc                          >  7:124656/1‑149 (MQ=255)                                                                                                                 ctTCGCGGGTAAACCCGCTCCTACGGG‑‑‑GGACCG‑CGCACGGTCCGCGCCTGTAGGA‑GCGGATTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCt                         >  8:226570/1‑149 (MQ=14)                                                                                                                    cgcgGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTgg                       >  7:149664/1‑148 (MQ=255)                                                                                                                            aaTCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGc               <  5:108749/148‑1 (MQ=255)                                                                                                                            aaTCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CACGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGc               <  3:298714/148‑1 (MQ=255)                                                                                                                             aTCCGCTCCTACAGGCGCGGACCGTTGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGcc              >  7:56886/1‑149 (MQ=255)                                                                                                                                 gCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGt                                                 <  7:71173/109‑1 (MQ=255)                                                                                                                                 gCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGt                                                 >  8:71173/1‑109 (MQ=255)                                                                                                                                     cTACAGGCGCGGACCG‑TGGGCGGTCC‑‑‑CCCGTAGTA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACAccc     <  6:173636/149‑1 (MQ=255)                                                                                                                                     cTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACAccc     >  1:110740/1‑149 (MQ=255)                                                                                                                                         aGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTg                        <  2:328208/126‑1 (MQ=255)                                                                                                                                           gcgcGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGAGGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTc  >  1:29840/1‑147 (MQ=255)                                                                                                                                             |                                                                                                                                                     GCAGCATGATTGCCCGACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTC  >  NC_002947/4896274‑4896557

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑