Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,030,748	A→G	7.4%	intergenic (+34/‑461)	PP_4433 → / → dadA‑I	amino acid MFS transporter/D‑amino acid dehydrogenase small subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,030,748	0	A	G	7.4%	151.3 / 2.6	54	intergenic (+34/‑461)	PP_4433/dadA‑I	amino acid MFS transporter/D‑amino acid dehydrogenase small subunit
Reads supporting (aligned to +/- strand):  ref base A (26/24);  new base G (2/2);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.13e-01

CCTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTATCTCTT  >  NC_002947/5030604‑5030895                                                                                                                                                  |                                                                                                                                                     ccTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCa                                                                                                                                                  <  7:22025/149‑1 (MQ=255)  cTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAg                                                                                                                                                 >  5:184415/1‑149 (MQ=255)         ctacATCATGGTTGCATCAGCACTTGGGATTATTGGGTTGTTCTTTGTGATGGAGACTAAAGGTTGCTCGATTCGCGGGGATGTAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCa                                                                                                                                           <  5:186468/148‑1 (MQ=255)         ctacATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTACAGAGCCTGGGT‑GCTGATTAGCAccc                                                                                                                                            <  2:165455/147‑1 (MQ=255)              tcatGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGt                                                                                                                                     <  4:189507/149‑1 (MQ=255)                      gCATCATCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAg                                                                                                                              <  3:42202/148‑1 (MQ=255)                       cATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCt                                                                                                                            >  2:90347/1‑149 (MQ=255)                        aTCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTc                                                                                                                           >  7:142429/1‑149 (MQ=255)                                   ggATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCg                                                                                                                 <  1:90347/148‑1 (MQ=255)                                              ttgttCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCa                                                                                                                         >  4:108234/1‑129 (MQ=255)                                              ttgttCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCa                                                                                                                         <  3:108234/129‑1 (MQ=255)                                                gttCTTTGTGATCGAGTCTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATATCCTAATAGGCAGATGGTATATAGCCTGGGT‑GCTAATCAGCACCCAGTCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCg                                                                                                    <  5:166131/148‑1 (MQ=255)                                                gttCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGa                                                                                                       <  5:199640/145‑1 (MQ=255)                                                gttCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGa                                                                                                       >  6:199640/1‑145 (MQ=255)                                                   cTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTa                                                                                                >  7:277663/1‑149 (MQ=255)                                                       gtgATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGt                                                                                             <  2:256385/148‑1 (MQ=255)                                                       gtgATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTATTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGt                                                                                             >  1:256385/1‑148 (MQ=255)                                                        tgATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCg                                                                                           <  6:184415/149‑1 (MQ=255)                                                            cGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCAccc                                                                                                                                            <  4:118929/96‑1 (MQ=255)                                                            cGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCAccc                                                                                                                                            >  3:118929/1‑96 (MQ=255)                                                                 cTAAAGGTTGCTCGATTCGGGGGGATGGAATAGCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCTGGCAAGCCGACCGGCTACGTCGATATAagca                                                                                  <  8:213846/149‑1 (MQ=255)                                                                 cTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAag                                                                                    >  6:260350/1‑147 (MQ=255)                                                                           cTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTa                                                                                                <  6:243492/125‑1 (MQ=255)                                                                           cTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTa                                                                                                >  5:243492/1‑125 (MQ=255)                                                                           cTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTc                                                                         >  6:47641/1‑148 (MQ=255)                                                                                 tCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACcctt                                                                  >  6:131180/1‑149 (MQ=255)                                                                                   gcgGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACccttc                                                                 >  1:88156/1‑149 (MQ=255)                                                                                   gcgGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCt                                                                          >  1:121175/1‑139 (MQ=255)                                                                                   gcgGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATACAGCCTGGGT‑GCTGATTAGCACCCa                                                                                                                                           <  8:143395/74‑1 (MQ=38)                                                                                   gcgGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATACAGCCTGGGT‑GCTGATTAGCACCCa                                                                                                                                           >  7:143395/1‑74 (MQ=38)                                                                                       ggATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCtttt                                                            >  4:114277/1‑149 (MQ=255)                                                                                         aTGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTa                                                          <  5:260350/149‑1 (MQ=255)                                                                                          tGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTAt                                                         <  3:114277/149‑1 (MQ=255)                                                                                           ggAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTAt                                                         >  2:306822/1‑148 (MQ=255)                                                                                              aTACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCt                                                      <  8:142429/148‑1 (MQ=255)                                                                                                  cTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGCCCGGCTACGTCGATATAAGCAGCAGCGCTCCACGCTTCGTTTTTATTCTT‑Atct                                                >  2:183816/1‑149 (MQ=255)                                                                                                           aaTAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTg                                       <  5:47641/149‑1 (MQ=255)                                                                                                              aaCCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACccttcct                                                               <  3:233422/123‑1 (MQ=255)                                                                                                              aaCCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACccttcct                                                               >  4:233422/1‑123 (MQ=255)                                                                                                                  tAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACATCTTGGCATCTg                                >  1:24883/1‑149 (MQ=255)                                                                                                                     tAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGcc                             <  8:277663/149‑1 (MQ=255)                                                                                                                       ggCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGccc                            <  1:306822/148‑1 (MQ=255)                                                                                                                                   agagCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTAATCTCACCTCTTGGCATCTGGCCCTGATAACa                    <  1:188227/145‑1 (MQ=255)                                                                                                                                   agagCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTAATCTCACCTCTTGGCATCTGGCCCTGATAACa                    <  1:192735/145‑1 (MQ=255)                                                                                                                                   agagCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACa                    >  2:192735/1‑144 (MQ=255)                                                                                                                                   agagCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACa                    >  2:188227/1‑144 (MQ=255)                                                                                                                                   agagCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTc               >  6:247541/1‑149 (MQ=255)                                                                                                                                      gCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTc            <  5:247541/149‑1 (MQ=255)                                                                                                                                       ccTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACAgt                  >  7:21583/1‑142 (MQ=255)                                                                                                                                       ccTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACAgt                  <  8:21583/142‑1 (MQ=255)                                                                                                                                       ccTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCg           >  4:272617/1‑149 (MQ=255)                                                                                                                                         tGGGT‑GCTGATTAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGc          >  5:188484/1‑148 (MQ=255)                                                                                                                                             t‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTAtct     >  1:78078/1‑149 (MQ=255)                                                                                                                                                 tAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTATCTCtt  >  3:169886/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                     CCTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGT‑GCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTT‑ATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTATCTCTT  >  NC_002947/5030604‑5030895

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: ‑