Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	56.1%	8.3 / 46.8	41	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (5/13);  new base T (23/0);  total (28/13)
Fisher's exact test for biased strand distribution p-value = 4.86e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.11e-05

ATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAAC  >  NC_000913/3206291‑3206577                                                                                                                                                  |                                                                                                                                                aTTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGAATTTTTcaaac                                                                                                                                             >  2:491207/1‑146 (MQ=255)   ttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTCCAGACaa                                                                                                                                          <  1:530626/150‑1 (MQ=255)    tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCACACaaa                                                                                                                                         >  2:291122/1‑150 (MQ=255)               tGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑TAATTTTTTCAGACAAATAaaaaaaat                                                                                                                               >  1:415350/1‑147 (MQ=255)                gCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTCCAGACAAATACAAAAACTGGa                                                                                                                            <  1:35770/151‑1 (MQ=255)                 ccATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                           <  2:518929/151‑1 (MQ=255)                     tCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTCCAGACAACTAaaaaaa                                                                                                                                 >  2:10966/1‑141 (MQ=255)                            tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAAATTTTCCTAACAaaaaaaaaaaaagggcgtggcct                                                                                                                    >  2:303664/1‑134 (MQ=255)                              tGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GACATTTTTCAGAAAAAAAAAAAAAATGGAGATTGCCa                                                                                                                    >  2:712986/1‑145 (MQ=255)                                    aaTATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCAAAAAAAAAAAAAAACTGGAG‑TTTTCATGTTTAGCg                                                                                                           >  2:387432/1‑147 (MQ=255)                                     atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCCGACAAAAACAAAAAAAGGAG‑TTGCCATTATGAggggaa                                                                                                        >  1:415079/1‑144 (MQ=255)                                          cattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GTAATTTTTCAAAAAAAAAAAAAAAATGGGG‑GTGTCCTTATGAGGGAAAAaaata                                                                                                  >  2:106720/1‑150 (MQ=255)                                            ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GGAATTTTTTAGACAAAAAACAAAAAAGGAG‑TTGGCatgatggggggaaacta                                                                                                    >  2:189657/1‑135 (MQ=255)                                            ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GCATTTTTTCAGAAAAATAAAAAAAAAGGAG‑GTGGCCTGATGAGGGGAAGtaataa                                                                                                 >  2:514640/1‑149 (MQ=255)                                              cTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCAAACAAAAACAAAAAATGGAG‑GTGCCCTGATGAGCGGAAGtaataa                                                                                                 >  1:289036/1‑147 (MQ=255)                                                tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCCGACAAAAACAAAAACTGGAG‑TTGGCCTGATGAGCGAAAGAAATAAACaa                                                                                             >  1:606977/1‑149 (MQ=255)                                                tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCCGAAAAAAAAAAAAAAAGGAG‑GTGGCATGATGAGCGAAAAGAATAAACaa                                                                                             >  1:523815/1‑149 (MQ=255)                                                      cgcgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCAGACAAAAAAAAAAAATGGGG‑TTGCCATGATGAGGGGAAGAAATAAACAAAAAGCAgg                                                                                     >  2:309738/1‑150 (MQ=255)                                                                cACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAAATTTTTCAAACAAATACAAAAAATGGAG‑TTGCCATGATGAGCGAAAGTAATAAACAAAAGGCAGTGAATAAAtt                                                                            >  1:132754/1‑150 (MQ=255)                                                                         ttAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCAGAAAAAAACAAAAAATGGAG‑TTGGCATGATGAGCGAAAATAATAAACAAAAAGCAGGGAATAAATTGACAgaga                                                                    >  1:189962/1‑149 (MQ=255)                                                                                 atatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCAGACAAATACAAAAAATGGAG‑GTGGCATGATGAGCGGAAGTAAAAAACAAAAAGCAGGGAATAAATTGAAAGAGATTGTCGCTa                                                           >  1:583102/1‑150 (MQ=255)                                                                                      cACGGTGGCAAAAAATATAACACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTCCAGACAAATACAAAAACTGTAG‑TTGCCATGATGATCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACtt                                                       <  2:76177/149‑1 (MQ=255)                                                                                         ggTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GGATTTTTTCAAACAAATACAAAAACTGGAG‑TTGGCATGATGAGGGAAAGGAATAAACCAAAGGCAGGGGATAAGTTGACAGAGATTTTTGCTAAAttt                                                      >  1:482222/1‑147 (MQ=255)                                                                                               aaaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCAAACAAATAAAAAAAATGGGG‑GTGCCATGATGAGGGGAAAGAATAAACAAAAAGCAGGGAATAAGATGACAGAGATTTTCGCTAACTTTAACGcc                                                >  1:710986/1‑147 (MQ=255)                                                                                               aaaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAAATTTTTCCGACAAAAAAAAAAAATTGAG‑TTTCCCTGATGGGCGGAAAGAATAAAAAAAAAGCAGTGAAAAAAATGACAGAGATTTTTGCTAACTTTACcccc                                                >  1:389983/1‑147 (MQ=255)                                                                                                aaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAAATTTTTCAAAAAAAAACAAAAACTTGAG‑TTGTCCTGATGAGGGAAAGTAATAAACAAAAAGCAGGGAAAAAATTGACAAAGATTGTTGGTTACTTTACCGCCa                                               >  2:211637/1‑147 (MQ=255)                                                                                                   aaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTc                                        <  2:350602/151‑1 (MQ=255)                                                                                                        aaaaCCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCAGACAAAAACAAAAACTGGGG‑TTGCCATGATGAGGGAAAGTAATAAACAAAAGGCAGGGGATAAATTGACAGAGATTGTTGCTAAATTTTCCGCCATGATTTTTAccc                                   >  1:566691/1‑151 (MQ=255)                                                                                                         aacccACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTCCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGTTTGTCGCTAACTTTACCGCCATGATTTCTACCCg                                  <  1:112763/148‑1 (MQ=255)                                                                                                            ccACATTTTTATTGGTAGTTTGTGGCGGT‑GAATTTTTCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTACCTTTACCGCCATGATTTCTACCCGAAt                               <  2:117889/151‑1 (MQ=255)                                                                                                               caTTTTTATTGGTATTTTGTGGCGGT‑GAATTTTTCCAGACAAATAAAAAAACGGGTT‑TTGCTATGATGAGCAAAATTAATAAGCAACAGGAATTCAATAATTTAACAGATATTTCCCATATCTTTACCGCCATTATTTCTACCCGAAt                               <  2:339442/148‑1 (MQ=255)                                                                                                                  ttttAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCAGAAAAATACAAAAAATTGGG‑TTGCCATGATGAGGGAAAGGAATAAACAAAAGGCAGGGGATAAGTTGACAGAGATTGTCGCTAAATTTAACCCCCTGATTTTTTCCCGAATGcc                            >  1:692840/1‑148 (MQ=255)                                                                                                                   tttAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCCGACAAAACAAAAAACTGGGG‑TTGCCATGATGAGGGGAAGGAATAAACAAAAGGCAAGGAATAAATTTAAAGAGAATGTCGCCAACTTTAACGCCACTAATTTTACCCGaaag                              >  2:547744/1‑143 (MQ=255)                                                                                                                    ttAGTGGTAGTTTGTGGCGGT‑GAATTTTTTCAGACAAATAAAAAAAATGGAG‑TTGCCATGATGAGCGAAAAGAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTAACGCCATGATTTTTACCCGAATGCCtgat                        >  1:266697/1‑150 (MQ=255)                                                                                                                    ttAGTGGTAGTTTGTGGCGGT‑GAATTTTTCCAGACAAATACAAAAACGGGAG‑TTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGTTTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgat                        <  1:176200/150‑1 (MQ=255)                                                                                                                          gTATTTTGTGGCGGT‑AATTTTTTCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCGAAAGAAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTACCTTTACCGCCATGATTTCTACCCGAATGCCTGATGACgt                   <  2:414857/149‑1 (MQ=255)                                                                                                                                tgtgGCGGT‑GAATTTTTCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGAt            <  1:22195/150‑1 (MQ=255)                                                                                                                                 gtgGCGGT‑GAATTTTTCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATa           <  2:145134/150‑1 (MQ=255)                                                                                                                                      ggT‑GAATTTTTCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTa      >  1:372010/1‑150 (MQ=255)                                                                                                                                        t‑GAATTTTTCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaa    >  1:698151/1‑150 (MQ=255)                                                                                                                                           aaTTTTTCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaaa   <  1:713756/149‑1 (MQ=255)                                                                                                                                           aaTTTTTCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAAc  >  1:341056/1‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                                ATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAATTTTTCCAGACAAATACAAAAACTGGAG‑TTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAAC  >  NC_000913/3206291‑3206577

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑