Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,444	0	T	A	26.1%	85.6 / 14.0	46	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (5/29);  new base A (12/0);  total (17/29)
Fisher's exact test for biased strand distribution p-value = 1.59e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAA  >  NC_000913/3206310‑3206576                                                                                                                                       |                                                                                                                                      ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACaaa                                                                                                                                  <  2:55021/140‑1 (MQ=255)   cacTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGAATTTTTCAGACAaaaaaaaaaa                                                                                                                                >  2:15301/3‑140 (MQ=255)      tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACAAAAACTg                                                                                                                             >  1:770359/1‑140 (MQ=255)       gCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTgg                                                                                                                            <  2:820988/140‑1 (MQ=255)       gCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTgg                                                                                                                            <  2:499647/140‑1 (MQ=255)        ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCCTACAAATAaaaaaaaagaa                                                                                                                           >  2:1157925/1‑135 (MQ=255)         tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑g                                                                                                                         <  1:1129656/140‑1 (MQ=255)           tGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑Gtt                                                                                                                       <  1:52328/140‑1 (MQ=255)             gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCCGACAAAAACAAAAAATGGA‑GGTgg                                                                                                                     >  1:425624/1‑139 (MQ=255)                 aaTATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCatg                                                                                                                 <  2:753698/140‑1 (MQ=255)                  atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCatga                                                                                                                <  1:761611/140‑1 (MQ=255)                  atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCatga                                                                                                                <  1:269841/140‑1 (MQ=255)                   tatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACAAAAAATGGA‑GTTGCCctgat                                                                                                               >  1:117898/1‑140 (MQ=255)                        attcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGA‑GGTGGCATGATGAggg                                                                                                          >  2:39360/1‑138 (MQ=255)                         ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGa                                                                                                         <  2:1085838/140‑1 (MQ=255)                              aTTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAAAAAAAAAAAAGGA‑GTTGGCATGATGAGCGgaaaga                                                                                                    >  2:851157/1‑137 (MQ=255)                               ttttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGAATTTTTTCCGAAAAAAAAAAAAAATAGA‑GGTTCCATGAATAGCGaaaaaaa                                                                                                   >  2:911519/1‑136 (MQ=255)                                 ttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGGATTTTTTCCGACAAAAACAAAAAATAGA‑GTTGCCCTGGTGAGGGCAAGgaata                                                                                                 >  1:548103/1‑140 (MQ=255)                                  tCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACAAAAAATGGA‑GGTGGCATGATGAGGGAAAAaaataa                                                                                                >  1:819827/1‑140 (MQ=255)                                    gcgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAACAAAAAATGGA‑GTTGCCATGATGAGCGAAAGtaaaaaaa                                                                                              >  1:501622/1‑138 (MQ=255)                                       ttGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAAc                                                                                           <  2:770359/140‑1 (MQ=255)                                          aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                                        <  2:116529/140‑1 (MQ=255)                                           ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGc                                                                                       <  2:800523/140‑1 (MQ=255)                                             cACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTACCATGATGAGCGAAAGTAATAAGCAACAGGCAg                                                                                     <  2:293643/140‑1 (MQ=255)                                               cGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTg                                                                                   <  1:595009/140‑1 (MQ=255)                                                   cTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATa                                                                               <  1:756485/140‑1 (MQ=255)                                                    tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAATGGA‑GTTGCCATGATGAGCGAAAAGAAAAAACAAAAAGCAGAGAaaaa                                                                              >  2:920156/1‑140 (MQ=255)                                                    tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATaa                                                                              <  1:966991/140‑1 (MQ=255)                                                    tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGAAAAAAACAAAAACAGGA‑GTTGCCCTGATGAGCGAAAGAAAAAAACAACAAGCAGGGAATaa                                                                              >  1:1029480/1‑140 (MQ=255)                                                      ttAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAATGGA‑GGTGCCATGATGAGCGAAAGGAAAAAACAACAAGCAGTGAaaaaat                                                                            >  1:1063703/1‑138 (MQ=255)                                                               tatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAgaga                                                                   <  1:15301/140‑1 (MQ=255)                                                                atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTTAGACAAAAAAAAAAAAAAGA‑GGTGGCATGATGGGGGAAAAAAAAAAAAAAAAAGGAGTGAATAAAATGACagaaaa                                                                  >  2:408899/1‑137 (MQ=255)                                                                atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAAAGGA‑GGTGGCATTATGAGCGAAAATAATAAACAACAAGCAGGGAAAAAGTTGACAgagaa                                                                  >  2:13515/1‑139 (MQ=255)                                                                atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGAt                                                                  <  1:538527/140‑1 (MQ=255)                                                                atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCCGACAAAAACAAAAAATGGG‑GGTGTCATAATTAGGGAAAAAAAAAAGAAAAAAGCAGAGAATAAAATGACAgagaa                                                                  >  2:908799/1‑139 (MQ=255)                                                                   cACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCTAACAAAAAAAAAAAAAAGA‑GGTGGCATGATGGGCGGAAGGAATAAAAAAAAAGCAGGGAAAAAATTTAAAgagaattt                                                               >  2:1215555/1‑136 (MQ=255)                                                                   cACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGAGGCGGTGAATTTTTTCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGt                                                               >  2:639226/1‑140 (MQ=255)                                                                      ggTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCTAACAAAAAAAAAAAATGGA‑GGTGCCATTATGAGGGAAAGGAAAAAACAACAAGCAGAGAAAAAGTTGGAAAAGAATGTctg                                                            >  2:292108/1‑138 (MQ=255)                                                                       gTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGAAAAAAAAAAAAAATGGA‑GTTGGCATGGTGAGGGGAAATAATAAAAAAAAAGCAGGGAAAAAAATGGCAGAGATTGTTGCt                                                           >  2:163986/1‑140 (MQ=255)                                                                       gTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCt                                                           <  2:649742/140‑1 (MQ=255)                                                                        tGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGAAAAAAAAAAAAAATAGG‑GGTGGCATGATGAGGGGAAAAAAAAAACAAAAAGCAGGGAAAAAATTGACAGAAAATGttggta                                                          >  2:538527/1‑135 (MQ=255)                                                                           cAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAAAAAAAAAAATGGA‑GGTGGCATGATGAGGGAAAGGAAAAAACAAAAAGCAAGGAATAAATTTACAGAGATTGTCGCTAACt                                                       >  2:811330/1‑140 (MQ=255)                                                                                    taAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGATTTTTTCCAACAAAAAAAAAAAATGGAGGTTGCC‑TGATGAGCGGAAAAAAAAAACAACAAGCAGGGAATAAATTGACAGAGAATGTCGCTAACTTTACCGccc                                              >  2:299031/1‑139 (MQ=255)                                                                                            caTTTTTAGTGGTAGTTTGGGGGGGTAAATTTTTCCAGAAAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAAAAAGCAACAGGCAGTGAAAAAGTTGACAGAGATTGTCGCTAATTTTACCGCCATGATTTCt                                      <  2:817945/140‑1 (MQ=255)                                                                                                  tAGTGGTAGTTTGTGGGGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGa                                <  2:67856/140‑1 (MQ=255)                                                                                                     acagaGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAGGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATg                             <  1:934499/136‑1 (MQ=255)                                                                                                       gTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGcc                           <  1:851157/140‑1 (MQ=255)                                                                                                         aGTTTGTGGCGGTAAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtg                         <  2:440012/140‑1 (MQ=255)                                                                                                             tgtgGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatga                     <  1:243442/140‑1 (MQ=255)                                                                                                                 gCGGTGAATTTTTCCAGACAAATAAAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACgtg                 <  1:920156/140‑1 (MQ=255)                                                                                                                  cGGTGAATTTTTTCCGACAAAAACAAAAAAAGGA‑GGTGGCATGATGAGCGGAAGGAATAAAAAACAGGCAGTGAATAAATTGACAAAGAATGTCGCTAAATTTTTCGCCATGATTTTTACCCGAATGCCTGATGACgtgg                >  2:1132541/1‑140 (MQ=255)                                                                                                                    gTGAATTTTTCCAGACAAAAACAAAAAATTGG‑GGTGGCATGGTGAGCGAAAGTAAAAAGGAAAAAGCAGGGAATAAATTGACAGAGAATTTTGCTAACTTTACCCCCATGATTTTTACCCGAATGCCTGATGACgtcttt              >  2:934499/1‑136 (MQ=255)                                                                                                                      gAATTTTTCCAGACAAATACAAAAACTGGG‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa            <  1:331642/140‑1 (MQ=255)                                                                                                                                aGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaaa  <  1:292108/140‑1 (MQ=255)                                                                                                                                aGAAAAATAAAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaaa  <  1:1215555/140‑1 (MQ=255)                                                                                                                                   cAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaaa  >  2:119708/1‑137 (MQ=255)                                                                                                                                   cAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaaa  <  1:119708/137‑1 (MQ=255)                                                                                                                                       |                                                                                                                                      TTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAA  >  NC_000913/3206310‑3206576

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: ‑