Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,444	0	T	A	21.6%	107.7 / 11.4	51	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (4/36);  new base A (11/0);  total (15/36)
Fisher's exact test for biased strand distribution p-value = 2.87e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGC  >  NC_000913/3206312‑3206580                                                                                                                                     |                                                                                                                                         cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAaaaaaaaaaa                                                                                                                                   >  2:28985/1‑140 (MQ=255) cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACaaaaa                                                                                                                                   >  1:740105/1‑140 (MQ=255)  ccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAAc                                                                                                                                  <  1:1173209/140‑1 (MQ=255)     gCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTgg                                                                                                                               <  2:195179/140‑1 (MQ=255)      ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAaaaaaaaaaaaaggg                                                                                                                              >  2:449540/1‑135 (MQ=255)       tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                             <  2:332375/140‑1 (MQ=255)       tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                             <  1:932885/140‑1 (MQ=255)       tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                             <  2:539656/140‑1 (MQ=255)         tGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAAACAAATAAAAAAAATagaggt                                                                                                                           >  2:112493/1‑138 (MQ=255)             gcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCa                                                                                                                       <  2:260327/140‑1 (MQ=255)             gcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCa                                                                                                                       <  1:112493/140‑1 (MQ=255)               aaTATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCatg                                                                                                                     <  2:262923/140‑1 (MQ=255)                       ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                             <  2:731245/140‑1 (MQ=255)                       ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                             <  2:740105/140‑1 (MQ=255)                       ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                             <  2:842432/140‑1 (MQ=255)                       ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                             <  1:958173/140‑1 (MQ=255)                           tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAATTGAGGTGCCCTGATGAGCGaaaaa                                                                                                         >  1:49466/1‑138 (MQ=255)                           tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATTGAGTTGGCATGATGAGGGGAAga                                                                                                         >  1:435116/1‑139 (MQ=255)                           tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAAAAAAAAAAATGGAGGTGCCCTGATGAGGGaaaaa                                                                                                         >  2:742883/1‑138 (MQ=255)                                   cgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCa                                                                                                 <  1:1043756/140‑1 (MQ=255)                                     ttGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAAc                                                                                               <  2:610434/140‑1 (MQ=255)                                     ttGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAAc                                                                                               <  1:1116681/140‑1 (MQ=255)                                     ttGATTCACGAACCTTTAAATACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAAc                                                                                               <  2:49466/140‑1 (MQ=255)                                        aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                                            <  1:770019/140‑1 (MQ=255)                                        aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                                            <  2:1163135/140‑1 (MQ=255)                                        aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                                            <  1:28985/140‑1 (MQ=255)                                         ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGc                                                                                           <  1:297238/140‑1 (MQ=255)                                            aCGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGAGGTGCCATGATGAGCGAAAAGAATAAACAACAAGCAgg                                                                                        >  1:708199/1‑139 (MQ=255)                                               aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                                     <  2:1106409/140‑1 (MQ=255)                                                  tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAATGGAGGTGCCATGATGAGCGAAAGTAAAAAACAACAAGCAGTGAATaa                                                                                  >  1:215274/1‑140 (MQ=255)                                                  agTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGAATTTTTTCATACAAAAAAAAAAAAAGGAGGTGCCCTGATGAGGGGAAGTAAAAAACAAAAAGCAGGGAaaaa                                                                                  >  2:1158810/2‑140 (MQ=255)                                                            atatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGATTTTTTCAGACAAAAACAAAAAAAGGAGGTGCCATGATGAGCGGAAAGAATAAACAACAAGCAATGAATAAATTGAAagag                                                                        >  2:217175/1‑140 (MQ=255)                                                            atatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGAGTTGTCATGATGGGGGGAAAGAATAAACAACAAGGAGAGAAAAAATTGAAagag                                                                        >  2:110562/1‑140 (MQ=255)                                                            atatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATAGAGGTGGCATCATGGGGGGAAGAAAAAAACAAAAAGAAGGGAAAAAATTGACagaa                                                                        >  2:494461/1‑139 (MQ=255)                                                              atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAAAACAAAAAAAAGGGGTGTCATGATGAGCGAAAAAAATAAAAAAAAGGCAGGGAATAAAGTTACAgagaa                                                                      >  2:113915/1‑139 (MQ=255)                                                                   cGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATGAGTTGACAGAGATTGTCg                                                                 <  2:1008738/140‑1 (MQ=255)                                                                   cGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCg                                                                 <  2:1008737/140‑1 (MQ=255)                                                                     gTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCCAACAAAAAAAAAAAAAGGGGGTGCCATGATGGGGGGAAAGAATAAAAAACAAGCAGTGAATAAGTTGACAGAGAATGTCGCt                                                               >  2:396747/1‑140 (MQ=255)                                                                     gTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCt                                                               <  1:113915/140‑1 (MQ=255)                                                                     gTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCt                                                               <  1:449540/140‑1 (MQ=255)                                                                      tGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAAAAAAAAAAATGGAGTTGCCATGATGAGGGAAAAAAAAAAACAAAAAGCAGAGAATAAAATTAGAAAGATTTTCGCTa                                                              >  2:1122255/1‑140 (MQ=255)                                                                         cAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAACAAAAAACGGAGGTGCCATGATGAGCGAAAGGAAAAAACAAAAAGGCGGGAATAAATTTACAGAGAATGTTGCCAACt                                                           >  2:219604/1‑140 (MQ=255)                                                                         cAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAAAAAAAAAAATGGAGTTGCCATGATGAGGGAAAGGAATAAACAAAAAGCAGGGAATAAAGTGAAAAAGATTGTTGCTaaat                                                           >  2:681356/1‑138 (MQ=255)                                                                              aaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGAAAAATAAAAAAACGGGAGTTGCCATGATGAGCGAAAGTAAAAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTAcc                                                      <  2:576125/140‑1 (MQ=255)                                                                                        cacaTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGAttt                                            <  1:217175/140‑1 (MQ=255)                                                                                        cacaTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGAttt                                            <  1:681356/140‑1 (MQ=255)                                                                                          caTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCt                                          <  2:1055366/140‑1 (MQ=255)                                                                                                 agggaatgTTGGTGGCGTAAAATTTTTCAAAAAAATTAAAAAACCAGAAGTTACCTTGATGAGCAAAATAAATAAAAAACAAAGGGTAAATAAGTTTACAGAAATTTTCGTTACTTTTTCCGCCATGATTTCTACCCGaa                                   <  2:235773/133‑1 (MQ=255)                                                                                                  gTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAAt                                  <  1:396747/140‑1 (MQ=255)                                                                                                   tGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATg                                 <  1:219604/140‑1 (MQ=255)                                                                                                     gTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGcc                               <  1:742883/140‑1 (MQ=255)                                                                                                       aGTTTGTGGCGGTGAATTTTTTCCGACAAAAACAAAAAATGGGGGTGGCATGGTGAGCGGAAAAAATAAACAACAAGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCCCCACGATTTCTACCCCAATGCCtg                             >  2:333033/1‑140 (MQ=255)                                                                                                          ttGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg                          <  1:844324/140‑1 (MQ=255)                                                                                                          ttGTGGCGGTGAATTTTTCCAGAAAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACGGGCAGTGAATAAGTTGACAGAGATTGTCGCTACCTTTACCGCCATGATTTCTACCCGAATGCCtgatg                          <  1:494461/140‑1 (MQ=255)                                                                                                          ttGTGGCGGTGAATTTTTCCAGAAAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg                          <  2:708199/140‑1 (MQ=255)                                                                                                             tgGCGGTGAATTTTTCCAGAAAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACg                       <  1:129791/140‑1 (MQ=255)                                                                                                               gCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACgtg                     <  2:388089/140‑1 (MQ=255)                                                                                                                 ggTGAATTTTTTCAGACAAATAAAAAAAAAGGAGGTGCCATGATGAGCGAAAAGAATAAGCAAAAAGCAGTGAAAAAATTGACAGAGATTGTCGCTAAATTTACCCCCATGATTTTTACCCCAATGCCTGATGACgtggg                   >  2:129791/1‑139 (MQ=255)                                                                                                                          ttCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGGGGATAAACt          >  1:1140928/1‑140 (MQ=255)                                                                                                                            ccAGAAAAATAAAAAAACGGGAGTGGCCATGATGAGGGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaa        <  1:1158810/140‑1 (MQ=255)                                                                                                                             cAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaa       >  2:315299/1‑140 (MQ=255)                                                                                                                                  aaaTACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGc  >  1:625193/1‑140 (MQ=255)                                                                                                                                     |                                                                                                                                         CCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGC  >  NC_000913/3206312‑3206580

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑