Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,366,771	C→A	15.8%	intergenic (‑82/+36)	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	4,366,771	0	C	A	15.8%	95.8 / 12.5	50	intergenic (‑82/+36)	dcuA/aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
Reads supporting (aligned to +/- strand):  ref base C (24/18);  new base A (3/5);  total (27/23)
Fisher's exact test for biased strand distribution p-value = 4.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.62e-01

CTATTCCCCCCAATCTGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCAACAGACCGCGTTCCAGAA  >  NC_000913_3_pae_tpiA/4366623‑4366919                                                                                                                                                      |                                                                                                                                                     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                                                                                          <  1:466506/77‑1 (MQ=37)                                                                                                                                  aataaaaaaGGCACG‑TCAGATGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAg                                                                                          >  2:466506/4‑80 (MQ=25)                                                                                                                                  aataaaaaaGGCACG‑TCAGATGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAg                                                                                          <  1:466262/77‑1 (MQ=25)                                                                                                                                   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)                                                                                                                                                      cTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCAACAGACCGCGTTCCAGaa  <  1:4493/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                     CTATTCCCCCCAATCTGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACG‑TCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCAACAGACCGCGTTCCAGAA  >  NC_000913_3_pae_tpiA/4366623‑4366919

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: ‑