Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,444	0	T	A	23.8%	78.2 / 14.1	42	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (7/25);  new base A (9/1);  total (16/26)
Fisher's exact test for biased strand distribution p-value = 2.08e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAA  >  NC_000913/3206305‑3206583                                                                                                                                             |                                                                                                                                            tGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAAt                                                                                                                                             >  1:1443043/1‑140 (MQ=255)       tCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTTAAAAAAAAACaaaa                                                                                                                                       >  2:1597836/1‑140 (MQ=255)       tCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AAATTTTTCAGACaaaaaaaaaa                                                                                                                                       >  1:821826/1‑140 (MQ=255)        cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACaaaaa                                                                                                                                      <  1:96873/140‑1 (MQ=255)           tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTCCGACAaaaaaaaaaaaag                                                                                                                                   >  1:1273533/1‑137 (MQ=255)            gCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTgg                                                                                                                                  <  1:328268/140‑1 (MQ=255)             ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑GATTTTTTCAGACAAATAAAAAAAATGGa                                                                                                                                 >  1:184353/1‑140 (MQ=255)                 ggCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAAAACAAAAACTGGAGTTg                                                                                                                             <  1:652284/140‑1 (MQ=255)                           tcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAg                                                                                                                   <  1:120515/140‑1 (MQ=255)                           tcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAg                                                                                                                   <  2:1010404/140‑1 (MQ=255)                            cattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTCAGACAAAAAAAAAAAATGGAGGTGGCATGATGAGc                                                                                                                  >  2:652284/1‑140 (MQ=255)                              ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                                <  1:107485/140‑1 (MQ=255)                              ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                                <  2:518513/140‑1 (MQ=255)                              ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                                <  2:160752/140‑1 (MQ=255)                              ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                                <  2:1443043/140‑1 (MQ=255)                              ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                                <  2:1159195/140‑1 (MQ=255)                              ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                                <  1:1823993/140‑1 (MQ=255)                              ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                                <  1:1408769/140‑1 (MQ=255)                                    ttttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTCAGACAAAAAAAAAAAATGGAGGTGCCCTGATGAGGggaaggaa                                                                                                          >  1:1663229/1‑140 (MQ=255)                                    ttttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AAATTTTTCAGACAAAAACAAAAAATGGGGGTGGCATGATGAGCggaaggaa                                                                                                          >  2:1139293/1‑140 (MQ=255)                                      ttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGG‑AAATTTTTCTCAGAAAAACAAAAACAGGAGTTGCCATGGAGAACGAAAGaaata                                                                                                        >  2:100765/1‑140 (MQ=255)                                       tCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTCAAACAAAAAAAAAAAAAGGGGGTGCCATGATGAGCGAAAAaaataa                                                                                                       >  2:107485/1‑140 (MQ=255)                                         gcgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTGGTTTGTGGCGGTG‑GAATTTTTCATACAAAAAAAAAAAAAGGGGGTGGTATTGTGGGCGGAAGtaataaaa                                                                                                     >  2:1408769/1‑138 (MQ=255)                                               aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                                               <  2:750993/140‑1 (MQ=255)                                                      aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                                        <  1:362211/140‑1 (MQ=255)                                                      aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                                        <  1:542124/140‑1 (MQ=255)                                                        cTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATa                                                                                      <  1:1794727/140‑1 (MQ=255)                                                         tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTCAGACAAAAACAAAAAATGGAGTTGCCATGATGAGCGAAAGTAATAAACAACAAGCAGTGAATaa                                                                                     >  1:1663048/1‑140 (MQ=255)                                                          gTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAg                                                                                    <  2:1626075/140‑1 (MQ=255)                                                           ttAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTCACACAAAAAAAAAAAATGGAGTTGCCATTATGAGAGAAAAAAAAAAAAAAAAAGCAGAGAATAAga                                                                                   >  2:1502230/1‑139 (MQ=255)                                                               ttACTTATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTCAGACAAAAACAAAAACTGGAGGTGGCATGATGAGCGAAAGAAAAAAAAAAAAAGCAGTGAAAAAGTTGaa                                                                               >  2:662635/1‑139 (MQ=255)                                                                     atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTCAGACAAAAAAAAAAAATGGAGGTGGCATGATGAGGGGAAAAAAAAAACAAAAAGGAGTGAATAAATTGACAgagaa                                                                         >  2:137087/1‑139 (MQ=255)                                                                     atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGG‑GATTTTTTCATACAAAAAAAAAAAAAGGAGGTGGCATGATGAGCGAAAATAAAAAAGAACAAGCCGGGAAAAAATTTAAAGAGAt                                                                         >  2:186026/1‑140 (MQ=255)                                                                                         taAAACCACATTTTTAGTGGTAGTTTGTGGTGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCa                                                     >  1:467144/1‑140 (MQ=255)                                                                                         aaaaaCCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGAAAAATACAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCATTGAATAAGTTGACAGAGTTTGTCGCTAACTTTACCGCCa                                                     <  2:1663048/139‑1 (MQ=255)                                                                                               cacaTTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCCA‑ACAAAAACAAAAAAAGGAGTTTGCATGATGTGCGCAAGAAAAAAACAAAAAGCAGTGGAAAAGGTGGCAGAGATTGTTGGTAAATTTTACGCCCTGAttt                                               >  2:364010/1‑140 (MQ=255)                                                                                                 caTTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATAAAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCt                                             <  1:364010/140‑1 (MQ=255)                                                                                                        aGTGGTAGTTTGTGGCGGTG‑ATTTTTTCCAGAAAAATAAAAAAACTGGATTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCCCTAACTTTACCGCCATGATTTCTACCCGaa                                      <  1:100765/140‑1 (MQ=255)                                                                                                        aGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGaa                                      <  1:605303/140‑1 (MQ=255)                                                                                                         gTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAAt                                     <  1:1502230/140‑1 (MQ=255)                                                                                                            gTAGTTTGTGGCGGTG‑ATTTTTACAAAAAAAATACAAAAGCGGGAGTTGCCAGGATGAGAAAAAGTAATAAGCACCGGGCAGTAAATAAGTTAAAAGGGATTCTGTCTACCTTTACCGCCATGATTTCTACCCGAATGcc                                  <  2:536122/140‑1 (MQ=255)                                                                                                            gTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGcc                                  <  1:186026/140‑1 (MQ=255)                                                                                                                 ttGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAGGTGGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg                             <  1:1614647/140‑1 (MQ=255)                                                                                                                      ggggTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGCCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACgtg                        <  1:1597836/138‑1 (MQ=255)                                                                                                                         gTG‑AAATTTTTCAGACAAAAAAAAAAAATGGGGTTGCCATGATGAGGGAAAGAAATAAGCAACAAGCAGTGAAAAAATTGACAGAGATTGTCGCTAACTTTTCCGCCCTGATTTTTACCCCAAAGCCTGATGACgtgggg                     >  2:1225766/1‑138 (MQ=255)                                                                                                                           g‑AATTTTTCCAAAAAAATACAAAAACGGGAGTGGCCGTGATGAGGGAAAGTAATAAGAAACAGCAAGTGAATAAGTTGACGGAGATTGTGGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa                   <  2:821826/140‑1 (MQ=255)                                                                                                                            aaaTTTTTCCAGAAAAATAAAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa                   <  2:66649/139‑1 (MQ=255)                                                                                                                              tttttcCCAGAAAAATAAAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATa                 <  1:1225766/139‑1 (MQ=255)                                                                                                                                     cAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaa          <  1:1139293/140‑1 (MQ=255)                                                                                                                                      aGACAAATACAAAAACGGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaaa         <  2:341477/140‑1 (MQ=255)                                                                                                                                      aGAAAAATAAAAAAACGGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAATTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaaa         <  2:1273533/140‑1 (MQ=255)                                                                                                                                       gACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACgtg                        >  2:588106/1‑124 (MQ=255)                                                                                                                                       gACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACgtg                        <  1:588106/124‑1 (MQ=255)                                                                                                                                         cAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAg      >  2:128117/1‑140 (MQ=255)                                                                                                                                          aaaTACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGc     >  1:1749843/1‑140 (MQ=255)                                                                                                                                            aTACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTa   >  2:279510/1‑140 (MQ=255)                                                                                                                                            aTACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTa   >  1:1308101/1‑140 (MQ=255)                                                                                                                                             tACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTaa  >  1:699376/1‑140 (MQ=255)                                                                                                                                             |                                                                                                                                            TGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTAA  >  NC_000913/3206305‑3206583

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑