Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,158,307	C→G	10.2%	P109R (CCT→CGT)	opuA →	glycine betaine ABC transporter ATP‑binding protein/permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,158,307	0	C	G	10.2%	144.0 / 7.8	49	P109R (CCT→CGT)	opuA	glycine betaine ABC transporter ATP‑binding protein/permease
Reads supporting (aligned to +/- strand):  ref base C (19/25);  new base G (2/3);  total (21/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.52e-01

GGCGAAGTGCTTTGCTTGATGGGTACATCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGCGCGGTGAGCCAGAAAGTACTCGCCGCACAGCGGCAC  >  NC_002947/3158174‑3158450                                                                                                                                      |                                                                                                                                                 ggCGAAGTGCTTTGCTTGATGGGTACATCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGC‑TGGCGCAGCGTAGGCTGCG‑TCaagct                                                                                                                                 <  7:156970/149‑5 (MQ=255) ggCGAAGTGCTTTGCTTGATGGGTACATCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGC‑TGGCGCAGCGTAGGCTGCG‑TCaagct                                                                                                                                 <  3:137151/149‑5 (MQ=255)    gAAGTGCTTTGCTTGATGGGTACATCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCg                                                                                                                               >  2:324385/1‑149 (MQ=255)      aGTGCTTTGCTTGATGGGTACATCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGt                                                                                                                             <  6:189939/149‑1 (MQ=255)              gcttGATGGGTACATCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAgcg                                                                                                                      >  1:66361/1‑148 (MQ=255)               cttGATGGGTACATCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTGCGCTGCG‑ACCGCAGCTGGCGCAgcgta                                                                                                                    <  8:184954/149‑3 (MQ=255)                     gggTACATCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCa                                                                                                              >  4:168893/1‑149 (MQ=255)                      ggTACATCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCAt                                                                                                             >  1:316290/1‑149 (MQ=255)                           aTCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACg                                                                                                                                              >  8:11045/1‑112 (MQ=255)                           aTCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACg                                                                                                                                              <  7:11045/112‑1 (MQ=255)                            tCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGtt                                                                                                       >  5:74330/1‑149 (MQ=255)                            tCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGtt                                                                                                       >  4:28494/1‑149 (MQ=255)                             ccGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCAt                                                                                                                   <  7:322020/136‑1 (MQ=255)                             ccGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCAt                                                                                                                   >  8:322020/1‑136 (MQ=255)                              cGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTc                                                                                                      >  7:264896/1‑148 (MQ=255)                                  aGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCTAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCa                                                                                                 <  2:66361/149‑1 (MQ=255)                                       cAATTCGACTTTGCTGCGCCACGGCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGGGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGGCGCAGCGCATCGGCATGGTGTTCCAGCATTTCg                                                                                            <  8:250116/149‑1 (MQ=255)                                         aGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGC‑TGGCGCAGCGTAGGCTGCGTCAAGCTGctcag                                                                                                                            >  2:87563/1‑111 (MQ=25)                                         aGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGC‑TGGCGCAGCGTAGGCTGCGTCAAGCTGctcag                                                                                                                            <  1:87563/115‑5 (MQ=25)                                                tttGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTtgctgc                                                                                   >  5:234238/1‑149 (MQ=255)                                                          cACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAg                                                                         <  3:6471/149‑1 (MQ=255)                                                           aCGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGc                                                                        <  2:98727/149‑1 (MQ=255)                                                              tCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTtgctgc                                                                                   <  3:294640/135‑1 (MQ=255)                                                              tCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTtgctgc                                                                                   >  4:294640/1‑135 (MQ=255)                                                                     gTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACa                                                              <  1:324385/149‑1 (MQ=255)                                                                        gATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAAc                                                            <  3:28494/148‑1 (MQ=255)                                                                          tAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTg                                                         >  5:35451/1‑149 (MQ=255)                                                                            gagCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGc                                                       <  6:35451/149‑1 (MQ=255)                                                                              gCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCt                                                     <  8:264896/149‑1 (MQ=255)                                                                               ccGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGc                                                                                                               >  8:249243/1‑90 (MQ=255)                                                                               ccGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGc                                                                                                               <  7:249243/90‑1 (MQ=255)                                                                                cGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTg                                                   >  1:328918/1‑149 (MQ=255)                                                                                    cagcGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGcccc                                               <  6:115184/149‑1 (MQ=255)                                                                                      gcggcgAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTg                                             <  5:358656/149‑1 (MQ=255)                                                                                       cggcgAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTgg                                            <  6:117054/149‑1 (MQ=255)                                                                                        ggcgAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGa                                           <  2:328918/149‑1 (MQ=255)                                                                                         gcgAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGaa                                          <  3:168893/149‑1 (MQ=255)                                                                                                 cTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGcgcg                                   <  6:234238/148‑1 (MQ=255)                                                                                                   cATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGCGCGGt                                 >  4:340170/1‑148 (MQ=255)                                                                                                    aTCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGCGCGGt                                 <  6:74330/147‑1 (MQ=255)                                                                                                    aTCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGCGCGGt                                 >  8:91990/1‑147 (MQ=255)                                                                                                     tCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGCGCGGt                                 >  4:114539/1‑146 (MQ=255)                                                                                                     tCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGCGCGGt                                 <  3:114539/146‑1 (MQ=255)                                                                                                          ggTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCt                                                                   <  7:197703/107‑1 (MQ=255)                                                                                                          ggTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCt                                                                   >  8:197703/1‑107 (MQ=255)                                                                                                            tGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGCGCGGTGAGCCAGaaa                       <  7:91990/149‑1 (MQ=255)                                                                                                              aGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGCGCGGTGAGCCAGAAAg                      <  2:316290/148‑1 (MQ=255)                                                                                                                           gctggcGCAGCGTAGGCTGCGTCAAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGCGCGGTGAGCCAGAAAGTACTCGCCGca           >  4:294204/6‑147 (MQ=255)                                                                                                                                 gCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGCGCGGTGAGCCAGAAAGTACTCGCCGCACAGCGGCAc  >  2:133543/1‑149 (MQ=255)                                                                                                                                      |                                                                                                                                                 GGCGAAGTGCTTTGCTTGATGGGTACATCCGGCAGCGGCAAGTCGACTTTGCTGCGCCACGTCAACCGGTTGATAGAGCCGAGCAGCGGCGAGGTGCTCATCGACGGTGAGGTCCTGAGCAGCTTGACGCAGCCTACGCTGCG‑CCAGCTGCGGTCGCAGCGCATCGGCATGGTGTTCCAGCATTTCGGTTTGCTGCCGCATCGAAGCGTGCTCGACAACGTGGCCTTGCCCCTGGAATTGCGCGGTGAGCCAGAAAGTACTCGCCGCACAGCGGCAC  >  NC_002947/3158174‑3158450

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: ‑