Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	29,496	0	T	A	42.0%	72.7 / 25.6	50	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
Reads supporting (aligned to +/- strand):  ref base T (27/2);  new base A (0/21);  total (27/23)
Fisher's exact test for biased strand distribution p-value = 3.76e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGAGGG  >  NC_000913/29352‑29646                                                                                                                                                  |                                                                                                                                                       gTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTACATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATaaaaa                                                                                                                                                   <  2:19199/150‑1 (MQ=255)   aaaTTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATc                                                                                                                                                >  1:117628/1‑151 (MQ=255)        ttGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGcc                                                                                                                                           >  2:686494/1‑151 (MQ=255)              aTTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTa                                                                                                                                       >  2:671504/1‑149 (MQ=255)                ttGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGtt                                                                                                                                   >  1:20278/1‑151 (MQ=255)                 tGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTg                                                                                                                                  >  1:362141/1‑151 (MQ=255)                 tGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTg                                                                                                                                  >  1:379156/1‑151 (MQ=255)                               cTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATACATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGccc                                                                                                                     >  2:164597/1‑150 (MQ=255)                                    cGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATAtct                                                                                                               >  1:82653/1‑151 (MQ=255)                                     tttttttttTAATGAAATCTTCTTGCTGCGCAAGCTTTTTCA‑AGAACAGGTTAGATAATTTTTTTGTCGTTTAATGCCTGTAAAACAGGCATGAGCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATAtct                                                                                                               <  2:139244/149‑1 (MQ=255)                                     gTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAATAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAATATGCATGAGCCACAATATAATATAATAAATCCCGCCATTAAGTTGACTTTTAGCGCACATAtc                                                                                                                >  2:287784/1‑149 (MQ=255)                                          tATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGATTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGa                                                                                                          >  1:267033/1‑150 (MQ=255)                                           aTTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAAt                                                                                                        >  1:149658/1‑151 (MQ=255)                                               cATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgccg                                                                                                    >  2:259733/1‑151 (MQ=255)                                               cATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgccg                                                                                                    >  2:578583/1‑151 (MQ=255)                                                aTGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgccgc                                                                                                   >  2:524932/1‑151 (MQ=255)                                                    aaTTTTCTTGCGGCCCAAG‑GTTTTCCAAAAACAGGTTAAATAATTTTTTTTTCATTAAAGCCCTGAAAAACAGGCATGACCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgcc                                                                                                     <  2:134572/145‑1 (MQ=255)                                                         tcttGCTGCGCAAGCTTTTCCC‑AAAACAGTTTAGATGTTTTTTTTGTCGCTTAATGCTTGAAAAACATGCAGGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTg                                                                                             <  1:698643/148‑1 (MQ=255)                                                            tgctgcGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGGGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGa                                                                                        >  1:234197/1‑150 (MQ=255)                                                                gcgcAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtc                                                                                   >  2:179613/1‑151 (MQ=255)                                                                 ctcatgctttcccc‑AAAACAGGTTAAATTTTTTTTTTCTCTCTTAATCCCTTAAAAACATGCATGGCCCAAAAAATAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtc                                                                                   <  2:511139/138‑1 (MQ=255)                                                                   cAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtcgtc                                                                                >  2:256431/1‑151 (MQ=255)                                                                     aGCTTTTTCA‑AGAACAGGTTAGATGATTTTTTTGTCTCTTAATGCTTAAAAAACATGAATGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAg                                                                                         <  1:129374/140‑1 (MQ=255)                                                                      gCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGt                                                                             >  1:114866/1‑151 (MQ=255)                                                                        gTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTa                                                                            >  2:618374/1‑150 (MQ=255)                                                                         ttttCC‑AGAACAGGTTAGTGGATTTTTTTTTCGTTTAATGCCTGAAAAACATGCATGAGCCAAAAAAAAATAAAAAAACCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTa                                                                            <  1:405191/149‑1 (MQ=255)                                                                          tttCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGc                                                                         >  2:336117/1‑151 (MQ=255)                                                                          ttccc‑AAAACAGTTAAGATGATTTTTTTGTCGTTAAATCCTTAAAAAACATGCATGAGCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAg                                                                          <  1:147281/147‑1 (MQ=255)                                                                                aaaaCAGGTTAGATGTTTTTTTTGTCGTTTAATGCCTAAAAAACATGCATGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGa                                                                      <  1:329205/147‑1 (MQ=255)                                                                                  aaCAGTTTAGATGTTTTTTTTGTCGCTTAATGCTTGAAAAACATGCAGGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAttt                                                                   <  1:229997/150‑1 (MQ=255)                                                                                  aaCAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTg                                                                  >  1:42619/1‑151 (MQ=255)                                                                                      ggTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAtt                                                              >  1:167819/1‑151 (MQ=255)                                                                                          aGATGTTTTTTTTGTCGCTTAATGCCTGAAAAACATGCATGAGCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGa                                                            <  1:601218/149‑1 (MQ=255)                                                                                          aGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAtt                                                          >  1:132997/1‑151 (MQ=255)                                                                                           gatgatCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAttt                                                         >  1:691160/1‑151 (MQ=255)                                                                                             ttatttttttGTCTATTAATTCTTGTAAAACATTCTTGACCCAAAAAATAATAAAAAAATTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAt                                                           <  2:630341/142‑1 (MQ=255)                                                                                                tttttttGTCTTTTAATGCCTGAAAAACATGCATGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGt                                                     <  1:448430/148‑1 (MQ=255)                                                                                                              atggcttgaaaaaCATGCTTGATCAAAAAAAAAAAATAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGaa                                         <  2:608903/139‑1 (MQ=255)                                                                                                              aatgcttaaaaaaGATCCATGAGCCAAAAAATAATAAAAAATACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATtgt                                            <  2:691193/136‑1 (MQ=255)                                                                                                                 gcttgaaaaaCATGCATGAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAat                                    <  1:30374/144‑1 (MQ=255)                                                                                                                       aaatCATGCATGCACCACAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCa                               <  2:619777/149‑1 (MQ=255)                                                                                                                       aaaaCATGCATGAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTGATATGc                                <  1:179659/148‑1 (MQ=255)                                                                                                                        aaaCATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAAt                            >  1:296562/1‑151 (MQ=255)                                                                                                                        aaaCATGCATGACCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAAt                            <  1:473637/151‑1 (MQ=255)                                                                                                                         aaCATGCAGGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATa                           <  1:681614/151‑1 (MQ=255)                                                                                                                            atgcatgAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATaa                          >  1:565351/1‑149 (MQ=255)                                                                                                                             tgcatgAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                        <  1:686734/150‑1 (MQ=255)                                                                                                                               caggaccaaaaaaaTAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtg                      <  1:318994/140‑1 (MQ=255)                                                                                                                                       aaaaaaaaaaaaaaaaaaTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagt                       <  1:393099/139‑1 (MQ=255)                                                                                                                                        caAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATAtt            >  1:347414/1‑151 (MQ=255)                                                                                                                                            aaaataAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTctct        <  1:671741/149‑1 (MQ=255)                                                                                                                                                tataAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATATCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATACCGTGAGTGAATATTCTCTgg      >  2:316883/1‑149 (MQ=255)                                                                                                                                                 ataAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGAgg   >  1:44353/1‑151 (MQ=255)                                                                                                                                                  taAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGAggg  >  1:566140/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                       GTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGAGGG  >  NC_000913/29352‑29646

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑