Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	21.3%	103.1 / 15.0	47	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (1/36);  new base T (10/0);  total (11/36)
Fisher's exact test for biased strand distribution p-value = 2.12e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGA  >  NC_000913/3206296‑3206566                                                                                                                                            |                                                                                                                                    gCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTc                                                                                                                                     <  1:2278141/140‑1 (MQ=255)     aaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGa                                                                                                                                 >  1:2040726/1‑140 (MQ=255)     aaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGa                                                                                                                                 <  1:86246/140‑1 (MQ=255)     aaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGa                                                                                                                                 >  2:711448/1‑140 (MQ=255)       cATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACa                                                                                                                               <  1:1579137/140‑1 (MQ=255)        aTTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACaa                                                                                                                              <  2:40382/140‑1 (MQ=255)         ttGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACaaa                                                                                                                             <  2:1225089/140‑1 (MQ=255)          tGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAAt                                                                                                                            >  1:2107688/1‑140 (MQ=255)            acagtCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATAc                                                                                                                          <  1:1165783/136‑1 (MQ=255)                    tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTg                                                                                                                  <  2:1281491/140‑1 (MQ=255)                      ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGa                                                                                                                <  2:2107688/140‑1 (MQ=255)                       tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                               <  2:1195345/140‑1 (MQ=255)                       tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                               <  1:986963/140‑1 (MQ=255)                         tGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGAggt                                                                                                             >  2:1569322/1‑138 (MQ=255)                          ggCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGAGGTg                                                                                                            >  2:1012656/1‑140 (MQ=255)                          ggCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAAAAAAAAAAATGGAGGTg                                                                                                            >  2:487056/1‑140 (MQ=255)                           gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAAAAAAAAATGGAGTTgg                                                                                                           >  2:986963/1‑139 (MQ=255)                           gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGc                                                                                                           <  1:1068840/140‑1 (MQ=255)                           gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCCTACAAAAAAAAAAAAAGGAGGTgt                                                                                                           >  2:1165783/1‑139 (MQ=255)                                atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAAAGGAGGTGCCatga                                                                                                      >  1:2790/1‑140 (MQ=255)                                atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCatga                                                                                                      <  2:2387815/140‑1 (MQ=255)                                atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCatga                                                                                                      <  1:1619805/140‑1 (MQ=255)                                atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAAACAAATAAAAAAAATGGAGGTGGCatga                                                                                                      >  2:1030921/1‑140 (MQ=255)                                atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGAATTTTTTCCGACAAATAAAAAAAAAGGAGGTGTCatgg                                                                                                      >  2:1068840/1‑139 (MQ=255)                                  attcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCatgatg                                                                                                    <  2:1814342/140‑1 (MQ=255)                                    tcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAg                                                                                                  <  1:598181/140‑1 (MQ=255)                                      attcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCg                                                                                                <  1:367869/140‑1 (MQ=255)                                       ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                               <  2:741534/140‑1 (MQ=255)                                           tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAAAAAAAAAAAAAAAATTGGGGTGCCAAGATGAGCGgaaaa                                                                                           >  2:1304498/1‑138 (MQ=255)                                             ttttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGAGTTTCCCTGATGAGCGGAAGtaa                                                                                         >  2:1819111/1‑140 (MQ=255)                                                     ttGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAAc                                                                                 <  1:1189660/140‑1 (MQ=255)                                                      tGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACa                                                                                <  1:1304498/140‑1 (MQ=255)                                                        aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAATACAAAAAATGGAGGTGCCATTGTGAGCGAAAATAATAAACaaaaag                                                                              >  2:974120/1‑136 (MQ=255)                                                         ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGc                                                                             <  1:711448/140‑1 (MQ=255)                                                          tCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCa                                                                            <  2:124613/140‑1 (MQ=255)                                                             cGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACAAAAAATGGAGTTGCCATGATGAGCGAAAGAAATAAACAACAAGCAGTg                                                                         >  1:2289395/1‑140 (MQ=255)                                                               aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCTAAAGTAATAAGCAACAGGCAGTGaa                                                                       <  1:487056/140‑1 (MQ=255)                                                               aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                       <  1:1012656/140‑1 (MQ=255)                                                               aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                       <  1:994273/140‑1 (MQ=255)                                                               aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                       <  1:1734550/140‑1 (MQ=255)                                                                   gTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAATGGAGTTGGCATGATGAGGGAAAATAAAAAAAAACAAGCAGTGAATaaa                                                                   >  2:2266682/1‑139 (MQ=255)                                                                    ttAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACAAAAAATGGAGTTGCCATGATGAGCGAAAGTAATAAACAAAAGGCAGTGAATAAGt                                                                  >  1:1559780/1‑140 (MQ=255)                                                                             tatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGTCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAgaga                                                         <  2:2075819/140‑1 (MQ=255)                                                                             tatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAgaga                                                         <  2:1960379/140‑1 (MQ=255)                                                                              atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAAAAAAAAATGGAGGTGCCATGATGAGGGAAAGTAATAAAAAAAAAGCAGGGAATAAGTTGACAgagaa                                                        >  2:65367/1‑139 (MQ=255)                                                                              atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGAt                                                        <  1:726961/140‑1 (MQ=255)                                                                                tCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAATAAAAAAAATGGAGTTGCCATGATGAGCGAAAATAATAAACAAAAAGCAGTGAAAAAAGTGACAGAGATTg                                                      >  2:726961/1‑140 (MQ=255)                                                                                   cGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCg                                                   <  1:1569322/140‑1 (MQ=255)                                                                                       ggCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTaa                                               <  1:1812026/140‑1 (MQ=255)                                                                                         cAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAATACAAAAAATGGAGATGCCCTGATGAGCGAAAGAAATAAACAACAGGCAGTGAATAAATTGACAGAGATTGTTGCTAACt                                             >  2:1662406/1‑140 (MQ=255)                                                                                         cAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGAAAAAAAAAAAAAATGGAGGTGGCATGATGAGCGAAAAAAAAAAACAAAAAGCAGGGAAAAAATTTACAGAGATTTTTGCTTACt                                             >  2:2348922/1‑140 (MQ=255)                                                                                                          caTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTACCTTTACCGCCATGATTTCt                            <  2:1065458/140‑1 (MQ=255)                                                                                                          caTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGAAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCt                            <  1:1030921/140‑1 (MQ=255)                                                                                                                  gtgtgattttGGGGCGGTGATTTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGAGGAGCGAAAGTAATAAGCAACAGGCAGTGAATAGGTTGACGGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAAt                    <  2:2075582/133‑1 (MQ=255)                                                                                                                  gTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAAt                    <  2:1893824/140‑1 (MQ=255)                                                                                                                  gTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAAt                    <  1:893476/140‑1 (MQ=255)                                                                                                                     gTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAATGGAGGTGCCATGATGAGCGAAAGTAATAAACAAAAAGCAGGGAAAAAATTGACAAAGATTGTCGCTAAATTTACCCCCATGATTTTTACCCCAATGcc                 >  2:893476/1‑140 (MQ=255)                                                                                                                     gTAGTTTGTGGCGGTGAATTTTTCCAGACAAAAAAAAAAACTGGAGTTGCCATGAAGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTATCTTTACCGCCATGATTTCTACCCGAATGcc                 <  2:2263331/140‑1 (MQ=255)                                                                                                                      tAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCt                <  1:648786/140‑1 (MQ=255)                                                                                                                          ttGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGAAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg            <  1:1121280/140‑1 (MQ=255)                                                                                                                            gtgGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGAc          <  1:2266682/140‑1 (MQ=255)                                                                                                                                    aattttttCCAGAAAAATACAAAAATGGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACGGGCAGTAAATAAGTTGACAGAGATTGTCGCTATCTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa  <  2:2376120/137‑1 (MQ=255)                                                                                                                                            |                                                                                                                                    GCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGA  >  NC_000913/3206296‑3206566

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑