Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	40.0%	60.2 / 30.2	55	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (8/25);  new base T (22/0);  total (30/25)
Fisher's exact test for biased strand distribution p-value = 4.79e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTA  >  NC_000913/3206287‑3206582                                                                                                                                                       |                                                                                                                                                    gtgtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCa                                                                                                                                                   <  2:231165/151‑1 (MQ=255)         cGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAAt                                                                                                                                            <  1:899896/150‑1 (MQ=255)          gCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACaaaaa                                                                                                                                           >  2:326036/1‑148 (MQ=255)            aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACaa                                                                                                                                        <  2:51470/151‑1 (MQ=255)                 aTTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑GATTTTTTCCGCCCAATAaaaaaa                                                                                                                                     >  2:206261/1‑149 (MQ=255)                   tGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTg                                                                                                                                  <  1:319447/150‑1 (MQ=255)                    gCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTgg                                                                                                                                 <  1:634675/150‑1 (MQ=255)                          cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCCGACAAAAACAAAAAAAGGAGTTGcc                                                                                                                          >  2:944293/1‑151 (MQ=255)                            cTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑GGTTTTTCCCGGcaaaaacaaaaaataaagatggcgt                                                                                                                        >  2:661061/1‑138 (MQ=255)                            cTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑GAGTTTTTCATAAAAATAAAAAAAATGGAGGTg                                                                                                                            >  1:190607/1‑147 (MQ=255)                            cTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCACACTAAAACAAAAAATGGaagt                                                                                                                             >  1:700139/1‑143 (MQ=255)                             tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCCGAAAAAAAAAAAAAATTGAGTTgtc                                                                                                                          >  1:12744/1‑146 (MQ=255)                                      gcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGaa                                                                                                              <  1:329906/151‑1 (MQ=255)                                         atatTCATTCTTATTTTCGCGTTGATTCACTAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGt                                                                                                           <  2:719600/151‑1 (MQ=255)                                                 tcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑GATTTTTTCAGACAAAAAAAAAAAAACGAGTTGGCATGATGAggggaaaaaata                                                                                                       >  1:752219/1‑136 (MQ=255)                                                  cTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGG‑AATTTTTCC‑TAAAAAAACAAAAACAGGGGTTTTCCTGATTGGCGAAAgctaaaa                                                                                                      >  1:230/1‑141 (MQ=255)                                                    tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCaa                                                                                                  <  2:838059/149‑1 (MQ=255)                                                     aTTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAg                                                                                               <  2:300446/151‑1 (MQ=255)                                                       tttCGCGTTGATTCACGAGCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGG‑AATTTTTTAAACCAAAAAAAAAAACAGAAGTT‑TCATGATGAGAGGAAGgaaaaaaaaa                                                                                                  >  1:885548/1‑142 (MQ=255)                                                       tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GTAATTTTTTAGAACAAAAAAAAAAAAAGGGGTGGCC‑TGATGGGGGGAAGAAAAAAacaaca                                                                                                >  1:808619/1‑148 (MQ=255)                                                        ttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑GATTTTTTCCGACAAAAACAAAAAATGGAGTTGCCATGATGAGCGGAAAaaataaaaaaaagg                                                                                              >  2:261004/1‑141 (MQ=255)                                                          cgcgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGt                                                                                          <  2:854886/151‑1 (MQ=255)                                                            cgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCCGACAAATAAAAAAAATGGAGGTGCCCTGATGAGGGGAAGTAATAAacaaca                                                                                                >  2:197372/1‑143 (MQ=255)                                                            cgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGC‑G‑TATTTTTTCATACAAATAAAAAAAATAAAGATGGCGTGGTGGGCGAAAGTAAAAAacaacaaggaggg                                                                                         >  1:1023003/1‑143 (MQ=255)                                                                 aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAg                                                                                   <  1:627890/151‑1 (MQ=255)                                                                   tCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGt                                                                                  <  1:127442/150‑1 (MQ=255)                                                                    cACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTg                                                                                <  1:1068999/151‑1 (MQ=255)                                                                     aCGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCACACAAAAAAAAAAAAAAGGGGTGGCATGATGAGGGGAAGAAAAAAACAAAAAGCAAGGAATaaaat                                                                                 >  2:386684/1‑146 (MQ=255)                                                                          cTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑GAATTTTTCAAAAAAAAAAAAAAAATGGAGTTGTCATGATGAGGGAAAATAATAAACAAAAAGAAGTGGAAAAGATGaaa                                                                             >  1:95201/1‑146 (MQ=255)                                                                           tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AAATTTTTCAGAAAAAAAAAAAAAAAGGAGGTTTCATGATGAGCGGAAGAAATAAACAACAGGCAGAGGAAAAATTGACa                                                                             >  1:380102/1‑147 (MQ=255)                                                                             ttAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGG‑G‑AATTTTTTCCTAAAAATACAAAAAAAGGAGGGGGCCTGATGGGAGAAAGGAAAAAACAAGAGGCAGTGGAAAAACTGACAgaga                                                                         >  2:1135200/1‑149 (MQ=255)                                                                                   aCATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCt                                                                 <  1:944236/151‑1 (MQ=255)                                                                                         tCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACtt                                                            <  1:618876/150‑1 (MQ=255)                                                                                            cGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTAc                                                         <  1:186235/150‑1 (MQ=255)                                                                                                      aaaTATAAAACCACATTTTTAGTGTGAGTTTTTGGCGGT‑G‑AATTTTTCTAAATAAATACAAAAACTGGAGTTGCAAAGTTACGCGAAAGTAATAAGAAACGGGCAGTAAATAATTTGCCAGGGATTGTCGCTATCTTTACCGCCATGAttt                                              <  2:375545/151‑1 (MQ=255)                                                                                                      aaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGG‑G‑GTTTTTTTCCGACCAAAAAAAAAAATTGAGGTGGCATGGTGAGGGGAAGATTTAAAAAAAAGGCAGGGGAAAAGTTTACAGAGAATGTCTCTAAATTTAACGcctt                                                   >  1:86840/1‑144 (MQ=255)                                                                                                            aaaaCCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAATAAAAAAAATGGAGGTGCCATGATGAGCGAAAGTAATAAACAACAGGCAGTGAATAAATTGACAGAGATTGTCGCTAACTTTACCGCCCTGATTTTTAccc                                        >  2:795697/1‑151 (MQ=255)                                                                                                            aaaaCCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAAAAAAAAAAGGGGGTGGCATGATGAGCGGAAAGAAAAAACAAAAAGCAGTGAAAAAATTGACCGAGATTGTCGCTAACTTTACCCCCACGATTTTTTccc                                        >  2:638157/1‑151 (MQ=255)                                                                                                            aaaaCCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCACACCAACAAAAAAACTGGAGGTGTCCTGGTGAGCGGAAGTAATAAGGAAAAAGCAGAGAATAAGGTGGAAGAGGTTGTCGGTAACTTTACCGTCATGATTTCt                                            >  1:216985/1‑147 (MQ=255)                                                                                                               aCCACATTTTTAGTGGTAGTTTGTGGCGGTGG‑AATTTTTCC‑GACAAAAAAAAAAAATTGAGTTGCCATGATGAGGGGAAAAAAAAAACAAAAAGGAGGGAAAAAATTGACAGAGATTGTCGCTAAATTTTCCGCCCAGATTTTTTccc                                        >  2:1144878/1‑148 (MQ=255)                                                                                                                 cacaTTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAACAAAAACCGGAGTTTCCATGATGAGCGGAAGGAATAAGCAACAGGCAGTGAATAAGGTGACAGAGATTGTCGCTAACCTTACCGCCCTGATTTTTACCCCaa                                     >  2:53189/1‑149 (MQ=255)                                                                                                                   caTTTTTAGTGGTAGTTTGTGGCGGG‑G‑AATTTTTCCAGACAAATAAAAAAAATAGGGGTTCCCTGATGAGAGAAAGGAAAAAACAAAAGGGAGTGAAAAAGATGACAGAGATTGTCGCTTAATTTATCGCCCTGATTTTTACCCGAATGcc                                 >  2:339073/1‑151 (MQ=255)                                                                                                                   caTTTTTAGTGGTAGTTTGTGGCGGG‑G‑AAATTTTTCCGACAAAAACAAAAAATGGAGTTTTCATGATGAGCGGAAAGAATAAAAAAAAAGGAGGGAATAAATTTACAGAGAATGTCGCTCAATTTACCCCCCTTAttttttacccaaag                                   >  1:322270/1‑138 (MQ=255)                                                                                                                      ttttAGTGGTATTTTGTGGCGGT‑G‑AATTTTTCAAGAAAAATAAAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACGGAGATTGTCGTTATCTTTACCGCCATGATTTCTACCCGAATGCCtg                               <  1:1262724/150‑1 (MQ=255)                                                                                                                      ttttAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtg                               <  2:752248/150‑1 (MQ=255)                                                                                                                      ttttAGTGGTAGTTGGTGGCGGT‑G‑AATTTTTCCAGACAAAAACAAAAACGGGAGTGGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACGGAGATTGTCGCTAACTTTGCCGCCATGATTTCTACCCGAATGCCtg                               <  2:119004/150‑1 (MQ=255)                                                                                                                           gTGGTAGTTTGTGGCGGT‑G‑ATTTTTTCCAAACAAATAAAAAAACGGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAATTTTACCGCCATGATTTCTACCCGAATGCCTGATGACg                         <  2:693085/151‑1 (MQ=255)                                                                                                                             ggTAGTTTGTGGGGGT‑G‑AATTTTCCCAGAAAAATAAAAAAACTGGATTGGCCATGATGACGGAAAGAAATAAGCAACAGGCAGTAAAAAATTGAAAAGAGATTGTCCTTATTTTTACCGCCATGATTTCTACCCGAATGCCtgatg                            <  1:1295633/146‑1 (MQ=255)                                                                                                                                 ttttGTGGCGGT‑T‑ATTTTTCCCAGAAAAATAAAAAACATGGAGTTCCAAGGATGAGCAAAAGTAATAACCAACTGGCTGTGAATAAGTTGCCAAATATTGCCTTTACTTTTCCCGCCATGATTTCTACCCGAATGCCTGATGACgt                        <  1:751200/145‑1 (MQ=255)                                                                                                                                         gggT‑A‑AATTTTTCCAGAAAAAAAAAAAAATGGGAGTTGCCATGATGAGCAAAAGTAAAAAGCAACAGGCGGTGAATAAGTTGACAGAGATTGTCGTTAATTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTa           <  1:326029/150‑1 (MQ=255)                                                                                                                                         cGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACt            >  1:105414/1‑150 (MQ=255)                                                                                                                                         cGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACt            >  2:246987/1‑150 (MQ=255)                                                                                                                                          ggT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTa           >  2:188084/1‑150 (MQ=255)                                                                                                                                                aaTTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAAc       >  2:839456/1‑150 (MQ=255)                                                                                                                                                     ttCCAGACAAATACAAAAACTGGAGTTGCCATGAGGAGCGAAAGTAAAAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGCCGTTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTa  <  1:22188/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                    GTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTA  >  NC_000913/3206287‑3206582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑