Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,793,752	G→T	18.6%	intergenic (+61/+66)	PP_2445 → / ← PP_2446	membrane protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,793,752	0	G	T	18.6%	101.5 / 14.1	43	intergenic (+61/+66)	PP_2445/PP_2446	membrane protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (15/20);  new base T (2/6);  total (17/26)
Fisher's exact test for biased strand distribution p-value = 4.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01

GCGGCCATGGCGTTCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAGGTGGTGTG  >  NC_002947/2793605‑2793894                                                                                                                                                       |                                                                                                                                               gCGGCCATGGCGTTCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTgg                                                                                                                                               >  1:149500/1‑149 (MQ=255) gCGGCCATGGCGTTCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTgg                                                                                                                                               >  2:245460/1‑149 (MQ=255)    gCCATGGCGTTCTCGTCGGCTATCGAGGTCCTGAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTGGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTgg                                                                                                                                               <  2:8788/146‑1 (MQ=255)    gCCATGGCGTTCTCGACGGCTATCGAGCTCCTAAACAACCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCAAAGCTATTCGCGTgg                                                                                                                                               >  1:8788/1‑146 (MQ=255)     ccATGGCGTTCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACt                                                                                                                                           <  2:149500/149‑1 (MQ=255)      cATGGCGTTCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTg                                                                                                                                          >  4:263339/1‑149 (MQ=255)       aTGGCGTTCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTgg                                                                                                                                         <  5:220471/149‑1 (MQ=255)             ttCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAAcgc                                                                                                                                   <  1:193185/149‑1 (MQ=255)                tcGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTgg                                                                                                                                         >  1:137660/1‑140 (MQ=255)                tcGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTgg                                                                                                                                         <  2:137660/140‑1 (MQ=255)                 cGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGaa                                                                                                                                >  2:5710/1‑148 (MQ=255)                  gACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGaa                                                                                                                                <  6:53807/147‑1 (MQ=255)                  gACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGaa                                                                                                                                <  3:970/147‑1 (MQ=255)                  gACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGa                                                                                                                                 <  3:123656/146‑1 (MQ=255)                  gACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATa                                                                                                                              <  2:88726/149‑1 (MQ=255)                  gACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CGCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGa                                                                                                                                 <  4:221215/146‑1 (MQ=255)                  gACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGGTGATGTAAAAAG‑‑GGGCGCCTCGCGCCCTCTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTTGCCAGTGCCACGCGAAt                                                                                                                               <  1:97210/149‑1 (MQ=37)                   aCGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATAc                                                                                                                             <  1:5710/149‑1 (MQ=255)                     ggCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTTGCCAGTGCCACGCGAATACCt                                                                                                                           <  6:268431/149‑1 (MQ=38)                     ggCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTTGCCAGTGCCACGCGAATACCt                                                                                                                           >  5:268431/1‑149 (MQ=38)                     ggCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTTGCCAGTGCCACGCGAATACCt                                                                                                                           <  4:103411/149‑1 (MQ=38)                     ggCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTTGCCAGTGCCACGCGAATACCt                                                                                                                           <  4:124530/149‑1 (MQ=38)                     ggCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCt                                                                                                                           <  5:308621/149‑1 (MQ=255)                      gCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCtg                                                                                                                          <  3:263339/149‑1 (MQ=255)                        cgtCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCtgtg                                                                                                                        <  7:355821/147‑1 (MQ=255)                          tCGAGGTCCTCAACATCCTGGCCCGTGCTGCGCGTTTGAAGCGTGAGGCGGCTTAAGGTTTATTTAAAAAGCCTGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTTGCCAGTGCCACGCGAATACCtgt                                                                                                                         <  1:114882/148‑1 (MQ=21)                          tCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCtgtg                                                                                                                        <  1:245460/147‑1 (MQ=255)                            gAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTg                                                                                                                                          <  3:226831/127‑1 (MQ=255)                            gAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTg                                                                                                                                          >  4:226831/1‑127 (MQ=255)                                   tCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAAcgc                                                                                                                                   >  2:83324/1‑127 (MQ=255)                                   tCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAAcgc                                                                                                                                   <  1:83324/127‑1 (MQ=255)                                                                                                                                gCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTg                   >  8:172484/1‑149 (MQ=255)                                                                                                                                   cGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCgg                <  7:172484/149‑1 (MQ=255)                                                                                                                                      tGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTgg             >  5:119571/1‑149 (MQ=255)                                                                                                                                        cacaGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGc            <  6:119571/148‑1 (MQ=255)                                                                                                                                         acaGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAg          >  3:188703/1‑149 (MQ=255)                                                                                                                                           aGGTATTCGCGTTGCCAGTGCCACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGc                  <  7:352515/139‑1 (MQ=37)                                                                                                                                           aGGTATTCGCGTTGCCAGTGCCACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGc                  >  8:352515/1‑139 (MQ=37)                                                                                                                                           aGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAggt        >  7:106178/1‑149 (MQ=255)                                                                                                                                           aGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAggt        >  2:321035/1‑149 (MQ=255)                                                                                                                                           aGGTATTCGCGTGGCACTGGCAACGCGAAAACCTCTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAggt        >  2:253238/1‑149 (MQ=255)                                                                                                                                             gTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAggtgg      >  6:368453/1‑149 (MQ=255)                                                                                                                                                ttCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGt               <  6:256746/137‑1 (MQ=255)                                                                                                                                                ttCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGt               >  5:256746/1‑137 (MQ=255)                                                                                                                                                ttCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAGGTGgtgt   >  4:96813/1‑149 (MQ=255)                                                                                                                                                ttCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAGGTGgtgt   <  8:106178/149‑1 (MQ=255)                                                                                                                                                  cgcgTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAGGTGGtgtg  >  6:85908/1‑148 (MQ=255)                                                                                                                                                       |                                                                                                                                               GCGGCCATGGCGTTCTCGACGGCTATCGAGGTCCTCAACATCCTGGCCCGTCGAGCGCGTTTGAAGCGTGAGGCGGCTGAAGGTTGATGTAAAAAG‑‑GGGCGCCTCGCGCCC‑CTCTTGCGGACAAGCCCGCTGCACAGGTATTCGCGTGGCACTGGCAACGCGAATACCTGTGCAGCGGGCTTGTCAGTCAGTGGGCTTCGGGAAATCCTGAGGTTAGCTCACCCCGGCATGCCGCCGGGGCCGTCTTACTGGCTGTGGCTTGGCGGGTGCCTGCGGTGGCAGGTGGTGTG  >  NC_002947/2793605‑2793894

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: ‑