Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,463,400	T→A	11.3%	intergenic (‑51/+48)	PP_4799 ← / ← lipA	muramoyltetrapeptide carboxypeptidase/lipoyl synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,463,400	0	T	A	11.3%	136.4 / 7.9	53	intergenic (‑51/+48)	PP_4799/lipA	muramoyltetrapeptide carboxypeptidase/lipoyl synthase
Reads supporting (aligned to +/- strand):  ref base T (24/23);  new base A (2/4);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.87e-01

CGCGCCGCGCCCGCCGGGGCGACAATGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGAAGCAACGTTCTTGAAGCCCATCTTGT  >  NC_002947/5463258‑5463542                                                                                                                                                |                                                                                                                                               cgcgccgcgcCCGCCGGGGCGACAATGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGgcg                                                                                                                                          >  2:272119/1‑149 (MQ=255)        cgcccgccGGGGCGACAATGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCg                                                                                                                                   <  6:198006/149‑1 (MQ=255)          cccgccGGGGCGACAATGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATAGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGc                                                                                                                                 <  1:216088/149‑1 (MQ=255)           ccgccgGGGCGACAATGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGCGCGCCCAAGGGCG‑GCATCg                                                                                                                                   >  2:57353/1‑146 (MQ=255)           ccgccgGGGCGACAATGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGCGCGCCCAAGGGCG‑GCATCg                                                                                                                                   <  1:57353/146‑1 (MQ=255)           ccgccgGGGCGACAATGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGCGCGCCCAAGGGCG‑GCATCGGCa                                                                                                                                <  2:125974/149‑1 (MQ=255)             gccgGGGCGACAATGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCg                                                                                                                                   >  1:212064/1‑144 (MQ=255)             gccgGGGCGACAATGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCg                                                                                                                                   <  2:212064/144‑1 (MQ=255)                  ggCGACAATGGCAAACCATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTGTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGCGCGCCCAAGGGcg‑gcatcggcatttttgt                                                                                                                         <  1:167625/149‑7 (MQ=38)                        aaTGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGc                                                                                                                   >  5:179278/1‑149 (MQ=255)                          tGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCg                                                                                                                    >  4:133038/1‑146 (MQ=255)                          tGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCg                                                                                                                    <  3:133038/146‑1 (MQ=255)                            gCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTa                                                                                                               <  7:188017/149‑1 (MQ=255)                                aaCATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCt                                                                                                           <  8:24450/149‑1 (MQ=255)                                     gCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGc                                                                                                            >  2:92004/1‑143 (MQ=255)                                     gCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTCGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGc                                                                                                            <  1:92004/143‑1 (MQ=255)                                           gCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGc                                                                                                 <  3:272895/148‑1 (MQ=255)                                                           gCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTgg                                                                                >  7:216064/1‑149 (MQ=255)                                                             aGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCagag                                                                                           <  7:172764/136‑1 (MQ=255)                                                             aGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCagag                                                                                           >  8:172764/1‑136 (MQ=255)                                                                   ggtTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGATAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTgg                                                                        >  6:127969/1‑149 (MQ=255)                                                                     ttGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGc                                                                      <  2:256972/149‑1 (MQ=255)                                                                        gAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCt                                                                                   <  4:97217/133‑1 (MQ=255)                                                                        gAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCt                                                                                   >  3:97217/1‑133 (MQ=255)                                                                        gAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGt                                                                          >  1:48564/1‑142 (MQ=255)                                                                        gAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGt                                                                          <  2:48564/142‑1 (MQ=255)                                                                        gAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCctg                                                                   >  5:39130/1‑149 (MQ=255)                                                                         aaGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCctgc                                                                  >  2:9862/1‑149 (MQ=255)                                                                                     cAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTgg                                                      <  3:11668/149‑1 (MQ=255)                                                                                          gaTCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGTCTCCGCTCTAGGCTAGAGCATATCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACg                                                  <  4:247436/147‑1 (MQ=255)                                                                                           aTCGCGGCTCCTTTCAGCGCATTGGACACAAACAAAAATGCCGATGG‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACgaa                                                <  6:179278/149‑1 (MQ=255)                                                                                            tCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACgaag                                               <  7:233562/149‑1 (MQ=255)                                                                                            tCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACg                                                  >  4:21406/1‑146 (MQ=255)                                                                                              gcgGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACgaagaa                                             <  1:272119/149‑1 (MQ=255)                                                                                                  cTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCa                                         <  5:127969/149‑1 (MQ=255)                                                                                                       tGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGc                                    >  6:122404/1‑149 (MQ=255)                                                                                                            cgcATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGcc                               <  1:9862/149‑1 (MQ=255)                                                                                                               aTTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAg                             >  4:39537/1‑148 (MQ=255)                                                                                                                      acaaacaaAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGaa                           >  4:303336/1‑143 (MQ=255)                                                                                                                      acaaacaaAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGaa                           <  3:303336/143‑1 (MQ=255)                                                                                                                        aaacaaaAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGAAGCAACGtt                   >  2:59779/1‑149 (MQ=255)                                                                                                                        aaacaaaAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGGACGAAGAACGCCCCAGCGGGCCAGAAGCAACGtt                   >  4:200633/1‑149 (MQ=255)                                                                                                                         aacaaaAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGAAGCAACGTTc                  <  3:39537/149‑1 (MQ=255)                                                                                                                           caaaAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGAAGCAACGTTCtt                >  8:88391/1‑149 (MQ=255)                                                                                                                               aaTGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGAAGCAACGTTCTTGAAg            <  6:39130/149‑1 (MQ=255)                                                                                                                                 tgccgatgc‑cgCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGAAGCAACGTTCTTGAAGcc          >  2:79733/1‑149 (MQ=255)                                                                                                                                    cgatgcgcGCCCAAGGGCG‑GCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGc                                <  4:212850/124‑1 (MQ=255)                                                                                                                                    cgatgcgcGCCCAAGGGCG‑GCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGc                                >  3:212850/1‑124 (MQ=255)                                                                                                                                    cgatgc‑cgCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGAAGCAACGTTCTTGAAGCCCa        >  4:179120/1‑148 (MQ=255)                                                                                                                                     gatgc‑cgCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTTCGAAGAACGCACCAGCGGGCCAGAAGGAACGTTCTTGAAGCCCATc      >  3:192322/1‑149 (MQ=255)                                                                                                                                     gatgc‑cgCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGAAGCAACGTTCTTGAAGCCCATc      <  5:122404/149‑1 (MQ=255)                                                                                                                                     gatgc‑cgCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGAAGCAACGTTCTTGAAGCCCATc      >  3:56627/1‑149 (MQ=255)                                                                                                                                           cgccCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGAAGCAACGTTCTTGAAGCCCATCTTGt  >  3:140162/1‑148 (MQ=255)                                                                                                                                                |                                                                                                                                               CGCGCCGCGCCCGCCGGGGCGACAATGGCAAAACATGCGTTGGCCGGCAGCGCGGCTGGCAGGGTGGGTTGGAAGGTTTTGGCGCAGTACATCGCGGCTCCTTGCAGCGCATTGGACACAAACAAAAATGCCGATGC‑CGCCCTTGGGCGCGCATCGGCATCTGTGGCTCCGCTCTAGGCTAGAGCATAGCTCAGAGCTTGATCTTGGCTTCGTGGGCCTGCTGGTCGGCGTGGTACGAAGAACGCACCAGCGGGCCAGAAGCAACGTTCTTGAAGCCCATCTTGT  >  NC_002947/5463258‑5463542

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑