Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	31.9%	67.8 / 26.4	47	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (1/31);  new base T (15/0);  total (16/31)
Fisher's exact test for biased strand distribution p-value = 2.13e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATA  >  NC_000913/3206300‑3206568                                                                                                                                          |                                                                                                                                      aaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGAA‑TTTTTccga                                                                                                                                    >  2:893661/1‑138 (MQ=255)         cATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACa                                                                                                                           <  1:492817/140‑1 (MQ=255)           ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTTAGACAaaaaaaaa                                                                                                                         >  2:485149/1‑140 (MQ=255)             cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACaaaaa                                                                                                                       <  1:849949/140‑1 (MQ=255)                tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑ATTTTTCAGACAAAAACAAAAAATg                                                                                                                    >  2:739162/1‑140 (MQ=255)                 gCTCTAGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTgg                                                                                                                   <  1:972942/140‑1 (MQ=255)                  ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCAGACAAATACAAAAACTggg                                                                                                                  >  1:823760/1‑139 (MQ=255)                  ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGa                                                                                                                  <  1:110929/140‑1 (MQ=255)                   tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTgggg                                                                                                                 <  2:823760/140‑3 (MQ=255)                   tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                 <  1:1232618/140‑1 (MQ=255)                   tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                 <  1:739162/140‑1 (MQ=255)                     tGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCAGACAAAAACAAAAAATGGAggt                                                                                                               >  1:741167/1‑138 (MQ=255)                     tGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCAGACAAAAAAAAAAAATGGAggt                                                                                                               >  2:849949/1‑138 (MQ=255)                     tGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGtt                                                                                                               <  2:1028457/140‑1 (MQ=255)                       gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTTCAACAAATAAAAAAAATGGGGtttg                                                                                                             >  2:972942/1‑138 (MQ=255)                       gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGC‑AAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCAGAAAAAAAAAAAAAATGGAGGTGcc                                                                                                            >  2:926512/1‑140 (MQ=255)                           aaTATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCatg                                                                                                         <  2:46401/140‑1 (MQ=255)                           aaTATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCatg                                                                                                         <  2:688615/140‑1 (MQ=255)                            atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GGA‑TTTTTTCTGAAAAATACAAAAAAAGGAGTTGGCatga                                                                                                        >  2:150234/1‑140 (MQ=255)                            atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCatga                                                                                                        <  1:706164/140‑1 (MQ=255)                                 cattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCAGACAAAAAAAAAAAAAGGAGTTGCCATGATGAgg                                                                                                   >  2:199263/1‑139 (MQ=255)                                   ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                 <  2:441980/140‑1 (MQ=255)                                     cTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCCGACAAAAAAAAAAAAAGGAGGTGCCCTGATGAGGGaaa                                                                                               >  2:1287738/1‑140 (MQ=255)                                     cTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCAGACAAATACAAAAAATGGAGTTGCCATGATGAGCGaaa                                                                                               >  1:925594/1‑140 (MQ=255)                                     cTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCAGACAAAAAAAAAAAAAAGAGGTGGCATGATGAGGGaaa                                                                                               >  2:706164/1‑140 (MQ=255)                                      ttATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAg                                                                                              <  2:721967/140‑1 (MQ=255)                                      ttATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAg                                                                                              <  2:1269627/140‑1 (MQ=255)                                       tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAAGTTTTTTCA‑ACAAAAAAAAAAACTAGAGGTGCCATTATgagagagaag                                                                                             >  2:445398/1‑136 (MQ=255)                                       tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                 >  1:1326429/1‑136 (MQ=255)                                       tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                 <  2:1326429/136‑1 (MQ=255)                                          tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGtaat                                                                                          <  1:785564/140‑1 (MQ=255)                                               cgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCa                                                                                     <  2:316035/140‑1 (MQ=255)                                                gTTGATTCACGAACTGTTAATTACATATTCACGGTGGC‑AAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAAc                                                                                   <  1:926512/140‑1 (MQ=255)                                                 ttGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAAc                                                                                   <  1:1044279/140‑1 (MQ=255)                                                   gATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GGG‑TTTTTTTTGACAAAAATAAAAAAACGCGGTGGCATGATGAGCGAGAAGAATAAGGaaaaa                                                                                 >  2:24978/1‑137 (MQ=255)                                                    aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                                <  1:485149/140‑1 (MQ=255)                                                         cGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTg                                                                           <  2:19522/140‑1 (MQ=255)                                                             cTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATa                                                                       <  1:445398/140‑1 (MQ=255)                                                             cTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATa                                                                       <  1:24978/140‑1 (MQ=255)                                                                ttAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCAGACAAAAAAAAAAAATGGAGGTGCCCTGATGAGCGGAAATAATAAAAAAAAAGCAGAGAaaaaaa                                                                    >  2:624611/1‑138 (MQ=255)                                                                   aTTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGa                                                                 <  1:940017/140‑1 (MQ=255)                                                                          atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑ATTTTTCAGACAAAAACAAAAAAAGGAGGTGCCATGATGAGGGAAAAAAAAAAACAACAAGCAGTGAAAAAAATTACAgagaa                                                          >  2:350961/1‑139 (MQ=255)                                                                              aCGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCCCACAAAAAAAAAAAATGGAGGTGCCCTGATGAGGGAAAGTAAAAAAAAAAAGGCAGTGGATAAGTTGACAGAGATTGTc                                                      >  2:479983/1‑140 (MQ=255)                                                                               cGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCg                                                     <  2:924366/140‑1 (MQ=255)                                                                                ggTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGc                                                    <  1:479983/140‑1 (MQ=255)                                                                                 gTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCt                                                   <  1:350961/140‑1 (MQ=255)                                                                                    gCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑ATTTTTCAAACAAAAAAAAAAAATGGAGGTTGCATGATGGGGGAAAAGAAAAAACAAAAAGCAGGGAAAAAATTGACAGAGATTGTCGCTaaa                                                >  2:416064/1‑139 (MQ=255)                                                                                              taAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAATTGGATTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGATAACTTTACCGCCa                                      <  1:1177121/140‑1 (MQ=255)                                                                                              aaaacCCACATTTTTAGTGGTATTTTGGGGCGGT‑AAA‑TTTTCCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAATTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCa                                      <  2:625498/139‑1 (MQ=255)                                                                                                    cacaTTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCAGACAAAAAAAAAAAATGGAGGTGGCCTGATGAGCGGAAGAAAAAAACAAAAAGCAGGGAAAAAAATGACAGAGAATGTCGCTAAATTTATCGCCCTGAttt                                >  2:1177121/1‑140 (MQ=255)                                                                                                      caTTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTTCAGACAAATACAAAAAATGGAGTTGGCATGATGAGCGAAAGTAATAAAAAACAAGCAGTGAATAAATTGACAGAGATTTTCGCTAAATTTACCCCCATGAttttt                              >  2:288236/1‑138 (MQ=255)                                                                                                             aGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGaa                       <  1:199263/140‑1 (MQ=255)                                                                                                                           gCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGGAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACgtg         >  1:724223/1‑140 (MQ=255)                                                                                                                           gCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCAAAATTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACgtg         <  1:150234/140‑1 (MQ=255)                                                                                                                              gT‑GAA‑TTTTTTCCGACAAATACAAAAAATGGAGGTGCCATGATGAGGGAAAGTAATAAGCAAAAGGGAGGGAATAAGTTGACAGAGATTGTCGCTAAATTTTACGCCATGATTTCTACCCGAAAGCCTGATGACgtgggg      >  2:1185065/1‑138 (MQ=255)                                                                                                                                   a‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATa  <  1:416064/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                      AACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATA  >  NC_000913/3206300‑3206568

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑