Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,017,222	Δ1 bp	7.5%	intergenic (+30/‑111)	udp → / → rmuC	uridine phosphorylase/DNA recombination protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,017,222	0	T	.	7.5%	182.8 / 8.3	53	intergenic (+30/‑111)	udp/rmuC	uridine phosphorylase/DNA recombination protein
Reads supporting (aligned to +/- strand):  ref base T (28/21);  new base . (2/2);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.06e-01

GTAGCGGGTGTTATCGTTAACCGCACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGATTTCTCAATCATGGTTTACGCAGTTATT  >  NC_000913/4017076‑4017365                                                                                                                                                    |                                                                                                                                                gTAGCGGGTGTTATCGTTAACCGCACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTc                                                                                                                                               >  1:179923/1‑149 (MQ=255)    gCGGGTGTTATCGTTAACCGCACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGc                                                                                                                                            <  2:179923/149‑1 (MQ=255)       ggTGTTATCGTTAACCGCACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCtt                                                                                                                                         >  4:77313/1‑149 (MQ=255)        gtgtTATCGTTAACCGCACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCGAACGCG‑TCGGCCttc                                                                                                                                        <  3:204977/149‑2 (MQ=255)        gtgtTATCGTTAACCGCACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCttt                                                                                                                                        >  2:443440/1‑149 (MQ=255)           ttATCGTTAACCGCACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGt                                                                                                                                     >  1:131304/1‑149 (MQ=255)             aTCGTTAACCGCACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTAt                                                                                                                                   >  2:131431/1‑149 (MQ=255)                 ttAACCGCACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTAttttt                                                                                                                               >  2:227003/1‑149 (MQ=255)                     ccGCACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGt                                                                                                                           >  1:474643/1‑149 (MQ=255)                        cACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAgc                                                                                                                        <  4:9944/149‑1 (MQ=255)                            cAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCGAACGCG‑TCGGCCttca                                                                                                                                       >  4:194622/1‑128 (MQ=255)                            cAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCGAACGCG‑TCGGCCttca                                                                                                                                       <  3:194622/130‑3 (MQ=255)                                aaGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCa                                                                                                                >  3:434882/1‑149 (MQ=255)                                     aTCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGaaa                                                                                                           <  1:15733/149‑1 (MQ=255)                                      tCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCGG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAAt                                                                                                          >  4:253867/1‑149 (MQ=255)                                      tCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAAt                                                                                                          >  2:373701/1‑149 (MQ=255)                                        ccGGATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGc                                                                                                        <  1:208352/149‑1 (MQ=255)                                         cGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGcc                                                                                                       <  2:474643/149‑1 (MQ=255)                                                   gaCGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTg                                                                                             >  3:69037/1‑149 (MQ=255)                                                     cGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGa                                                                                           <  1:227003/149‑1 (MQ=255)                                                          aaacaaacCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGttt                                                                                      <  4:434882/149‑1 (MQ=255)                                                           aacaaacCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTg                                                                                     >  3:222821/1‑149 (MQ=255)                                                            acaaacCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCtt                                                                                                                                         >  4:222046/1‑96 (MQ=255)                                                            acaaacCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCtt                                                                                                                                         <  3:222046/96‑1 (MQ=255)                                                             caaacCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTa                                                                                   <  2:330618/149‑1 (MQ=255)                                                                        ccATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTc                                                                        >  2:64958/1‑149 (MQ=255)                                                                          aTGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGc                                                                                                        <  4:120684/115‑1 (MQ=255)                                                                          aTGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGc                                                                                                        >  3:120684/1‑115 (MQ=255)                                                                                    aaTCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCgg                                                            <  1:64958/149‑1 (MQ=255)                                                                                           gtggAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGt                                                                                    <  2:377479/118‑1 (MQ=255)                                                                                           gtggAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGt                                                                                    >  1:377479/1‑118 (MQ=255)                                                                                            tggAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGt                                                                                                                                                 >  4:234955/1‑56 (MQ=255)                                                                                            tggAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGt                                                                                                                                                 <  3:234955/56‑1 (MQ=255)                                                                                              gAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAgttgtt                                                  >  4:307011/1‑149 (MQ=255)                                                                                                aGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGc                                                >  4:18091/1‑149 (MQ=255)                                                                                                              tgctgTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTtg                                  >  2:58882/1‑149 (MQ=255)                                                                                                               gctgTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTtgt                                 <  1:131431/149‑1 (MQ=255)                                                                                                                  gTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGa                              <  2:131304/149‑1 (MQ=255)                                                                                                                    aaTTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAACTGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTATGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGAtt                            >  2:461546/1‑149 (MQ=255)                                                                                                                      ttctcttctcCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGa                              >  2:360239/1‑145 (MQ=255)                                                                                                                      ttctcttctcCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGa                              <  1:360239/145‑1 (MQ=255)                                                                                                                      ttctcttctcCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGATTtc                          >  2:201272/1‑149 (MQ=255)                                                                                                                          cttctcCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGATTTCTCaa                      <  1:373701/149‑1 (MQ=255)                                                                                                                           ttctcCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTAtt                                                                    >  2:54673/1‑102 (MQ=255)                                                                                                                           ttctcCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTAtt                                                                    <  1:54673/102‑1 (MQ=255)                                                                                                                               ccTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGATTTCTCAATCATg                 <  1:443440/149‑1 (MQ=255)                                                                                                                                cTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGAtt                            <  3:386660/137‑1 (MQ=255)                                                                                                                                cTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGAtt                            >  4:386660/1‑137 (MQ=255)                                                                                                                                   tCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAgttgtt                                                  >  2:157847/1‑112 (MQ=255)                                                                                                                                   tCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAgttgtt                                                  <  1:157847/112‑1 (MQ=255)                                                                                                                                   tCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGATTTCTCAATCATGGttt             >  4:284596/1‑149 (MQ=255)                                                                                                                                      aaaGGCCGAACGCG‑TCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGATTTCTCAATCATGGTTTACg          >  4:198556/2‑149 (MQ=255)                                                                                                                                      aaaGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGATTTCTCAATCATGGTTTACg          >  3:298118/2‑149 (MQ=255)                                                                                                                                         ggCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGATTTCTCAATCATGGTTTACGCAg       >  2:225368/1‑149 (MQ=255)                                                                                                                                               aCGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGATTTCTCAATCATGGTTTACGCAGTTAtt  <  3:17418/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                GTAGCGGGTGTTATCGTTAACCGCACCCAGCAAGAGATCCCGAATGCTGAGACGATGAAACAAACCGAAAGCCATGCGGTGAAAATCGTGGTGGAAGCGGCGCGTCGTCTGCTGTAATTCTCTTCTCCTGTCTGAAGGCCG‑ACGCGTTCGGCCTTTTGTATTTTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCAACTGGACGTTTGTACAGCACAATTCTATTTTGTGCGGGTAAGTTGTTGCGTCAGGAGGCGTTGTGGATTTCTCAATCATGGTTTACGCAGTTATT  >  NC_000913/4017076‑4017365

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑