Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,366,770	T→G	14.4%	intergenic (‑81/+37)	dcuA ← / ← aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	4,366,770	0	T	G	14.4%	90.6 / 11.7	50	intergenic (‑81/+37)	dcuA/aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
Reads supporting (aligned to +/- strand):  ref base T (24/18);  new base G (3/4);  total (27/23)
Fisher's exact test for biased strand distribution p-value = 6.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.75e-01

CCTATTCCCCCCAATCTGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCAACAGACCGCGTTCCAGA  >  NC_000913_3_pae_tpiA/4366622‑4366918                                                                                                                                                      |                                                                                                                                                     ccTATTCCCCCCAATCTGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCAt                                                                                                                                                      <  1:384170/149‑1 (MQ=255)  cTATTCCCCCCAATCTGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGCAAAAAGGCACG‑TCATc                                                                                                                                                     >  1:212417/1‑149 (MQ=255)        cccccAATCTGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTCTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCAGATGACGt                                                                                                                                               <  1:5627/149‑1 (MQ=255)          gtcAATCTGGCGCCCAAGAAGATCGCAAGCAAAACTATGATGAGTTCTACAACTAGCATATTGGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGc                                                                                                                                             <  2:565543/147‑1 (MQ=255)          cccAATCTGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGc                                                                                                                                             >  1:502502/1‑149 (MQ=255)            cAATCGGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTTTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCt                                                                                                                                           <  2:277167/149‑1 (MQ=255)             aaTCTGGCGCCCAAGATGATCGCCTGCTAAACTTTGTTGAGTTCTACAACTATCTTATTAGCCTTCTTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCAGATGACGTGCCtt                                                                                                                                          <  2:112309/149‑1 (MQ=255)                   gcgcCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCATTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTCCTGCTCACAAGAAAAAAGGCCCG‑TAATCTGACGAGCCTTTTTTAt                                                                                                                                    >  1:413277/1‑149 (MQ=255)                       ccAAGAAGCTCGCCACCAAAACTATGATGTGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGt                                                                                                                                <  1:315390/149‑1 (MQ=255)                             acaTCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTAcc                                                                                                                          <  1:123550/147‑1 (MQ=255)                                  gcaaGCAACACTATGGTGATTCCTACGACGAGCGTCTGAGCCTGCGCATTTTTTTAACAAGTTGATAGTAGTTTGTTCTTTTTATTTTACAGCTCATAAGACAAAAGGCACG‑TCGTCTGACGTGCCTTTTTTATTTGTACTACCCCGTa                                                                                                                     <  2:21278/146‑1 (MQ=255)                                      gCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGAt                                                                                                                 >  1:672028/1‑149 (MQ=255)                                        aaaaCTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGACTTTTTTATTTGTACTACCCTGTCCGAGTa                                                                                                               >  1:163729/1‑149 (MQ=255)                                          aaCTATGATCAGTACTACACCTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACt                                                                                                             <  1:10777/149‑1 (MQ=255)                                            cTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGG‑ACGCCCTTCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGt                                                                                                           >  1:135192/1‑149 (MQ=255)                                             tATGATTAGTTCTACAACCAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGtt                                                                                                          <  1:278673/149‑1 (MQ=255)                                                cttgaTTTCTACAACTATCATATTAGGCTCCCTCCTTTTTTTACAAGTTTTAATTAGATTGTTATTTTTAAGTTACGCCTCACTATAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGc                                                                                                       <  2:220591/147‑1 (MQ=255)                                                  tgaGTTCTACAACTAGCATATTAGCCTTCCGTGTTTTTTAACAAGTTGATATTAGTTTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTCACTTGCCTTTTTTATTTGTACTACCCTGTTCGATTAATGTTCGCtt                                                                                                     >  2:31819/1‑149 (MQ=255)                                                        cTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTCCTGTTCGCTTtcatca                                                                                               >  1:144869/1‑149 (MQ=255)                                                                 gCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGTCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTATTCCGTATATCGt                                                                                      >  2:381218/1‑149 (MQ=255)                                                                    tatTAGCCTTCCTTGTTTTTTAACAAGTTGCTATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAAGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACTATTACTGTTCGCTTTAGTCAGTATAGCGtttt                                                                                   >  1:137308/1‑149 (MQ=255)                                                                      ttAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCCGTTTAGCGTTTTGc                                                                                 >  1:341049/1‑149 (MQ=255)                                                                      ttAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTAATCAGTATAGCGTTTTGc                                                                                 >  1:518300/1‑149 (MQ=255)                                                                         gCCTTCCTTGTTTTTTGACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAGAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCttt                                                                              >  1:640700/1‑149 (MQ=255)                                                                            ttccttGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTTCTTTTTa                                                                           >  1:385935/1‑149 (MQ=255)                                                                                ttGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTACGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACTATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTCAGcc                                                                       >  2:698116/1‑149 (MQ=255)                                                                                    tttttAACAAGTTGATATTAGACTGTTATTTTTCAGTGACTGCTCACAAGTAAAAATGCACG‑TCACATAATGTGCGTTTTTTGTTGTTACTTCCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGt                                                                   <  1:170573/149‑1 (MQ=255)                                                                                          aCAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCa                                                             <  1:594288/149‑1 (MQ=255)                                                                                                   tatTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAGAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTAGGATTACTGTTCGCTTTCATCAGTATAGCGTTTTTCTTTGTAAGCCGGGTGCGTATGATTCTGTa                                                    >  2:15856/1‑149 (MQ=255)                                                                                                       atatgcttATTTTGAATTTACTGCTCTCAAGAAAAAAGTCACG‑TCATCTGACGGGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTGTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGga                                                <  2:395018/143‑1 (MQ=255)                                                                                                        gATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAATATCGCTGTTTGCTTTGTAAGCCGGGTCCATCAGATTCTGTACGgag                                               >  1:39988/1‑149 (MQ=255)                                                                                                         tttGGTATTTGTAAGTTTCTGCTCATAAGAAAAAAGGCACG‑TCATCTGACGTGCTTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGgaga                                              <  2:331035/148‑1 (MQ=255)                                                                                                         atggTTATTTTTAAGTTACTTCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGGACGgaga                                              <  2:308208/146‑1 (MQ=255)                                                                                                             ttATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGATGTGCCTTTTTTATTTGTACTACCCTGTAGGATTGCTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTAAATAGGATTCTGTGCGGTGAAAat                                          >  1:81317/1‑149 (MQ=255)                                                                                                                 ttttAAGTTTCTGGTCACAAAACAAAAGGCCCT‑TCATCTGACGTGCCTTATTTATTTGTACTACCGTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGTGAAAATATCg                                      <  2:315222/149‑1 (MQ=255)                                                                                                                     aaGTTACTGCGCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCaa                                  <  2:411149/149‑1 (MQ=255)                                                                                                                       gTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGt                                >  2:548244/1‑149 (MQ=255)                                                                                                                       gTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGt                                >  1:623009/1‑149 (MQ=255)                                                                                                                           cTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGTCTGTTTTATTTGGTCTTCCCTGTACGATTACTTTTCGCTTTCATTAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCg                            <  1:239642/149‑1 (MQ=255)                                                                                                                           cTGCTAACAAGAAAAAAGGCGCG‑TCGTCTGACGTGGCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCg                            <  1:673737/149‑1 (MQ=255)                                                                                                                              cTCACAAGAAAAAAGCCACG‑CCATCTTACGTGCCTATTTTATATGTACTACCCTGTACGATTACTGTTGGCTGGCATCCGAGAAGGGTTTTGCGTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCtt                         <  1:170925/149‑1 (MQ=255)                                                                                                                                  aaataaaaaaGGCACG‑TCAGATGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGCGACAATATCGTCAAGTTCCGCTTCAGt                     >  2:311721/5‑149 (MQ=39)                                                                                                                                   aataaaaaaGGCACG‑TCAGATGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAg                                                                                         >  2:466262/4‑80 (MQ=25)                                                                                                                                   aataaaaaaGGCACG‑TCAGATGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAg                                                                                         >  2:466506/4‑80 (MQ=25)                                                                                                                                   aataaaaaaGGCACG‑TCAGATGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAg                                                                                         <  1:466262/77‑1 (MQ=25)                                                                                                                                   aataaaaaaGGCACG‑TCAGATGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAg                                                                                         <  1:466506/77‑1 (MQ=37)                                                                                                                                    aGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCa                   >  1:606423/1‑149 (MQ=255)                                                                                                                                     gAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTTTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCaa                  >  1:141471/1‑149 (MQ=255)                                                                                                                                      aaaaaaGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTCCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTTTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCaca                 >  2:523928/1‑147 (MQ=255)                                                                                                                                            ggCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTTCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCAACAGAcag           >  2:728220/1‑147 (MQ=255)                                                                                                                                                cG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCACCAGACCGCGtt       <  1:459680/149‑1 (MQ=255)                                                                                                                                                      tCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCAACAGACCGCGTTCCAGa  >  1:179177/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                                     CCTATTCCCCCCAATCTGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCAACAGACCGCGTTCCAGA  >  NC_000913_3_pae_tpiA/4366622‑4366918

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑