Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	29,486	0	C	A	41.8%	102.2 / 25.1	55	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
Reads supporting (aligned to +/- strand):  ref base C (25/7);  new base A (0/23);  total (25/30)
Fisher's exact test for biased strand distribution p-value = 1.13e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGTTGTTTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAAT  >  NC_000913/29339‑29633                                                                                                                                                      |                                                                                                                                                    ttgttgTTTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACaa                                                                                                                                                   >  2:823718/1‑150 (MQ=255)   gttgttTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACaaaa                                                                                                                                                 <  2:460393/150‑1 (MQ=255)     tgttTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAaata                                                                                                                                               <  2:181632/150‑1 (MQ=255)      gttTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAaataat                                                                                                                                             <  1:386811/151‑1 (MQ=255)              gTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATaaaaa                                                                                                                                      <  2:751656/150‑1 (MQ=255)                     ttGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGcc                                                                                                                              >  1:457976/1‑151 (MQ=255)                     ttGACCATTTAGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGc                                                                                                                               <  1:303665/150‑1 (MQ=255)                      tGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAaat                                                                                                                                                >  1:224979/1‑132 (MQ=255)                      tGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAaat                                                                                                                                                <  2:225019/132‑1 (MQ=255)                       gACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCAt                                                                                                                            >  2:461300/1‑151 (MQ=255)                                     tttttttCTTCTCTTTTTTTTTTCAGGCAATCTTCGTGCGGCGCAAGCTTTTCCCAAAACAGGTTAGTGGA‑TTTTTTTTTCTTTTAGT‑CCGTTAAAAACTGCCGGAACCCAAAAAAAAAAAAAAAAAACCCCGCCATTAAGTTGACtttt                                                                                                               <  2:547882/149‑1 (MQ=255)                                     tttttttCTCCTTTTTTTATTTTAATAAAATCTTTTTGCTGCAAAAGCTTTTCCAAAAACAGTTTAAATAT‑TTTTTTTTTCGTTTATTCCTTAAAAAATTTGAATG‑CCCAAAAAAATAATAAAAAAACTCCCGCCATTAAGTTGACtt                                                                                                                 <  1:205919/147‑1 (MQ=255)                                      ttttttCTGTTCTTTTTTATTTCATGCATTTTTCTTGGTGCGAAAGCTTTTTCCAGAACAGTTTAAATGA‑TTTTTTTTTCTCTAAATCCTTAAAAAACATGAATG‑AGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTa                                                                                                              <  2:72124/150‑1 (MQ=255)                                      ttttttCTGCTCTTTTTTTTTTCATGAATTCTTCTTGCTGCGCAAGCTTTTTCAAGAACAGGTTAG‑TGATTTTTTTTGTCTCTTAATCCTTGAAAAACATGCATG‑AGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACtttt                                                                                                               <  2:587661/149‑1 (MQ=255)                                      ttttttCTGCTCTTTTTTTTTTAATAAATTCTTCTTGCTGCGCAAGTTTTTTCAAAAACAGGTTAGATTA‑TTTTTTTGTCGTTTAATGCTTTAAAAACATGCATG‑ACCAAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACt                                                                                                                  <  1:968778/146‑1 (MQ=255)                                        ttttCTTCTGTTTTTTATTTCATGCATTCTTTTTGCCGCAAAAGCTTTTACCAAAAATGGTAAAATAA‑TTTTTTTCTCTTTAAATCCTTAAAAAAAATGAATG‑CCCAAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAgc                                                                                                            <  1:139101/150‑1 (MQ=255)                                        ttttCTGCTCGTTTTTTTTTCATGCAATCTTCTTGCTGCGAAAGCTTTTTCCAGAACAGTTTAGATGA‑TTTTTTTGTCGTTTAATGCCTAAAAAACATGCATG‑AGCCAAAAAATAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAgc                                                                                                            <  2:3942/150‑1 (MQ=255)                                              gCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCat                                                                                                      >  2:313283/1‑150 (MQ=255)                                                tCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATAtc                                                                                                   >  2:645112/1‑151 (MQ=255)                                                    ttttttttCATGCTATTTCCTTACGGGGCACTTGTCTCCAAGAACCGGTTAGACTA‑TCTTTTTATCGTTTATGCCCTTTAAACCCTGCATG‑TCCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                <  2:585262/150‑1 (MQ=255)                                                    ttttATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                >  1:702675/1‑150 (MQ=255)                                                     tttATTTCATGAATTCTTTTTGCGGCAAAGGCTTTTCCAAGAACAGTTAAGATGA‑TTTTTTTGTCGCTAAATGCTTGAAAAACATGCAGG‑GGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCa                                                                                               <  2:753848/150‑1 (MQ=255)                                                          ttCATGCATTCTTTTTGCTCCGCAAGCGTTTCCCAAAACATGTTAAATGT‑TTTTTTTGTCGTTTAATCCTTAAAAAACTGGCATG‑ACCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATg                                                                                          <  2:590540/150‑1 (MQ=255)                                                                     tttttGCGGCGCAAGCTTTTCCCAAAACGGGTTAGATAT‑TTTTTTTGTCGCTAAATGCCTAAAAAACTTGCATG‑AGCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGccgccg                                                                                    <  2:213932/142‑1 (MQ=255)                                                                     ttcttccccagcAAGGTTTTTCCAAAAGAGTTTGGATCT‑TTTTTTTGTGATTTATTCCGTAAAAAACTTGCAGG‑ACCAAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGtt                                                                                  <  2:474487/137‑1 (MQ=255)                                                                     ttcttGCTGCGCTAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGcc                                                                              >  1:876814/1‑151 (MQ=255)                                                                     ttcttGCTGCGCAGGCTTTTCCCAAAACAGGTTAGATGA‑TTTTTTTGCCGTTTATTGCCTTAAAAACATGCATG‑AGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACCTTTAGCGCCCATATCTCCAGAATGccgccg                                                                                    <  2:225649/145‑1 (MQ=255)                                                                     ttcttGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGcc                                                                              >  2:579763/1‑151 (MQ=255)                                                                      tcttGCTGCGCAAGCTTTTCCCAAAACAGTTTAGTGGA‑TTTTTTTGTCTCTTAATGCCTGAAAAACTGCCAGG‑ACCAAAAAAATAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGttt                                                                                 <  2:911196/147‑1 (MQ=255)                                                                       cttGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGcc                                                                              >  1:855726/1‑149 (MQ=255)                                                                                 aaggttttaCCAGAATGGGTTAGTTGA‑TTTTTTTTTCGCTTAATCCCTGAAAAAAACGCAGG‑AGCCAAAAAATAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtc                                                                      <  2:798738/142‑1 (MQ=255)                                                                                 aaGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtcgtcg                                                                  >  1:149687/1‑151 (MQ=255)                                                                                     ttttcCCAGAACAGTTTAGTTGA‑TTTTTTTGTCGTTTAATGCTTGAAAAACATGCAGG‑AGCAAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGt                                                                <  2:540266/148‑1 (MQ=255)                                                                                       tttCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGc                                                            >  2:775248/1‑151 (MQ=255)                                                                                         tCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGc                                                            >  2:909760/1‑149 (MQ=255)                                                                                          ccAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGc                                                            >  1:500979/1‑148 (MQ=255)                                                                                           cAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGc                                                            >  2:852346/1‑147 (MQ=255)                                                                                            aGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCCCAAAATAATATACAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTACAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAtt                                                       >  1:799490/1‑151 (MQ=255)                                                                                              aaCAGGTTAGATGA‑TTTTTTTGTCGCTTAATGCCTGAAAAACATGCATG‑ACCCAAAAAATAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAttt                                                      <  2:687493/150‑1 (MQ=255)                                                                                               aCAGGTTATATGT‑TTTTTTTGTCCCTTAATGCGTGTAAAACATGCATG‑ACCCAAAAAAAAATAAAAAAACTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGc                                                    <  2:398491/151‑1 (MQ=255)                                                                                                cAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGc                                                    >  1:969742/1‑150 (MQ=255)                                                                                                 aGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAt                                                  >  1:445919/1‑151 (MQ=255)                                                                                                    ttAGATAT‑TTTTTTTGTCGCTTATTCCCTGTAAAACATGCATG‑ACCAAAAAAATATAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCa                                                   <  1:874322/147‑1 (MQ=255)                                                                                                     tAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAt                                              >  2:460741/1‑151 (MQ=255)                                                                                                             tCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtc                                       >  1:44922/1‑151 (MQ=255)                                                                                                             tCTTTTTGTCGCTAATTGCTTTAAAAACATGCAGG‑ACCAAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTAc                                          <  2:232146/148‑1 (MQ=255)                                                                                                               tttttGTCGTTTAATGCCTAAAAAACATGCATG‑ACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtc                                       <  2:849894/149‑1 (MQ=255)                                                                                                               tttttGTCGCTTAATCCCTAAAAAACATGAATG‑ACCAAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtc                                       <  2:637059/149‑1 (MQ=255)                                                                                                                ttttGTCGTTTAATGCCTGAAAAACAGGAATG‑GCCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtcat                                     <  2:364605/150‑1 (MQ=255)                                                                                                                           aaTGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAAtt                          >  1:188901/1‑150 (MQ=255)                                                                                                                               ccTGAAAAACACGCAGG‑GCCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAatat                     <  2:431570/151‑1 (MQ=255)                                                                                                                                   tAAAACATGCATG‑AGACACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTTCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCa                  >  1:798910/1‑150 (MQ=255)                                                                                                                                     aaaCATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAAt               >  2:39251/1‑151 (MQ=255)                                                                                                                                      aaCATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAAt               >  2:570225/1‑150 (MQ=255)                                                                                                                                                 acaagcaAAATACAAAAAAAAACTCCGTCATTAAGTTGCCTCTTAGCGACGATATCTCCAGATTGCCGCCGTTTGACTGAAAATCATCGGTCAGCAGATAGGCATGGATTTACGTCATCATTGTGAATTAAGATGCAAATaaaa           <  1:548716/139‑2 (MQ=255)                                                                                                                                                   ccACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAat  >  2:388979/1‑151 (MQ=255)                                                                                                                                                      |                                                                                                                                                    TTGTTGTTTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGA‑TCTTTTTGTCGCTTAATGCCTGTAAAACATGCATG‑AGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAAT  >  NC_000913/29339‑29633

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑