Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,665,702	0	C	A	42.3%	70.1 / 29.4	52	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
Reads supporting (aligned to +/- strand):  ref base C (26/4);  new base A (0/22);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.11e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTT  >  NC_000913/3665552‑3665845                                                                                                                                                       |                                                                                                                                                aGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGc                                                                                                                                                 >  1:165838/1‑151 (MQ=255) aGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGc                                                                                                                                                 <  1:673589/151‑1 (MQ=255)  gTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGc                                                                                                                                                 >  1:738640/1‑150 (MQ=255)    gatgaACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaa                                                                                                                                               >  2:461328/1‑150 (MQ=255)        aaCGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAcc                                                                                                                                          >  1:262505/1‑151 (MQ=255)           gAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAgg                                                                                                                                       <  2:383285/151‑1 (MQ=255)                   aagaaACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGcc                                                                                                                               >  1:141398/1‑151 (MQ=255)                    agaaACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGcc                                                                                                                               >  1:638788/1‑150 (MQ=255)                      aaaCTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCAt                                                                                                                             <  1:36432/150‑1 (MQ=255)                           tttttATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAAt                                                                                                                       >  1:723726/1‑151 (MQ=255)                               tATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCg                                                                                                                   >  2:646916/1‑151 (MQ=255)                               tATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCg                                                                                                                   >  1:343377/1‑151 (MQ=255)                                aTGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCg                                                                                                                   >  2:105598/1‑150 (MQ=255)                                  gtgCATAAAGATTTAATCCCTCCTCCTTGAGCATCGGGAAAAATAATGAAAGCGTGTCCCTTGACACGAATAAAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCg                                                                                                                   <  1:45970/148‑1 (MQ=255)                                      aTGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTc                                                                                                             >  1:462164/1‑150 (MQ=255)                                      aTGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTc                                                                                                             >  1:222011/1‑150 (MQ=255)                                      aTGAAAATTAAATGCCTCCCCCTGGAGCATCGGAAAAAATAATAAAAGCGTGTCCCTTAACACAAAAAAAAAATTTTCACCCCACTTATCTTCTCAATTTTGGTTTGCATCCGAAAAAACCAGGCCACCGCCATTAAAATAGCGATATTc                                                                                                             <  2:93017/150‑1 (MQ=255)                                          atattaaaccccccctcttTGACCATCGGGAAAAAAAATAAAGGCGTGCCCTTTGACACAAATAAAAAATTTCCACCACACTTACCTACAAAATTTGGGCTTGCTCCCGAAAAAACCAGGTCCCCGCCATTAAAATAGCGATAtt                                                                                                              <  2:260299/132‑1 (MQ=255)                                             tttaagccatcctcttTGAGAATCGGGAAAAAAAATAAAAGCGTGTCCTTTGACACAAATAAAAAATTTTCAACCCTCTTATCTACTCGAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt                                                                                                       <  1:109257/140‑1 (MQ=255)                                               tAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAAcc                                                                                                   >  1:693245/1‑151 (MQ=255)                                                       cctcctTGAGCATCGGGAAAAAAAATAAAAGCGTGTCCCTTGACACGAATAAAAAATTTTCAACACCTTTATCTCCTCAAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga                                                                                            <  1:348864/150‑1 (MQ=255)                                                            ttGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatat                                                                                      >  2:635569/1‑151 (MQ=255)                                                                gCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAttt                                                                                  >  2:172519/1‑151 (MQ=255)                                                                    cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGt                                                                              >  1:25302/1‑151 (MQ=255)                                                                     gggAAAAAAAATGAAAGCGTGTCCCTTGACACAAATAAAAAATTTTCAACACATTTATCTACTCAATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAttt                                                                                  <  1:305565/146‑1 (MQ=255)                                                                     gggAAAAAAAATAAAAGCGTGCCCCTGGACACAAATAAAAAATTTTCAACACCCTTATCTACAAAATTTTGGTTTGCACCAGAAAAAACGGGGACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGt                                                                              <  2:78396/150‑1 (MQ=255)                                                                     ggaaaaaaTAATGAAAGCGTGTCCCTTGACAAAAATAAAAAATTTTAAACACCCTTATCTACTCAATTTTGGCTTGCACCCGAAAAAACCAGGACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGt                                                                              <  2:516339/145‑1 (MQ=255)                                                                        aaaaaaaaTAAAAGCGTGTCCCTTGACACAAAAACAAAATTTTCAACCCATTTATCTACCCGAATTTGGCTTGCACCCGAAAAAACCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtt                                                                           <  1:371351/148‑1 (MQ=255)                                                                        aaaaaTAATAAAAGCGTGTCCTTTGCCAAAAATAAAAATTTTCCAACACCTTTATCTACTAAATTTTGTTTTGCACCAGAAAAAACAGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtt                                                                           <  2:425656/148‑1 (MQ=255)                                                                           aataatGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCAt                                                                       >  1:133185/1‑151 (MQ=255)                                                                              aatAAAAGCGTGTCCTTTGACACAAATAAAAAATTTTCACCCCCCTTTTCTACTAAATTTTGGTTTCCACCCAAAAAAACAGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa                                                                      <  2:259948/149‑1 (MQ=255)                                                                              aacaaaaTCGTCTCCTTTAACACAAATAAAAAATTTTCAACACCATTATCTAGGCGATTTTGGCTTCCCCCCAAAAACACCAGGTCACAGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACg                                                                    <  2:447846/147‑1 (MQ=255)                                                                               atGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGc                                                                   >  2:100169/1‑151 (MQ=255)                                                                                  aaaGCGTGTCCCTTGACACAAATAAAAAATTTCCAACACATTTATCTCCTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAt                                                                <  1:362542/151‑1 (MQ=255)                                                                                    aGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAtt                                                               >  1:653791/1‑150 (MQ=255)                                                                                     gCGTGCCCCTTGACACAAATAAAAAATTTTCAACACACTTATCTCCTCGAATTTGGCTTGCACCCGAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAg                                                             <  1:703165/151‑1 (MQ=255)                                                                                             cTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTcc                                                     >  1:698824/1‑151 (MQ=255)                                                                                              ttGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTccc                                                    >  1:294599/1‑151 (MQ=255)                                                                                               tGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTccc                                                    >  2:563246/1‑150 (MQ=255)                                                                                                 acacAAAAAAAAAATTTTCAACCCATTTATCTACTCGAATTTGGCTTCCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCa                                                   <  1:520089/149‑1 (MQ=255)                                                                                                     gAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGt                                                >  2:488419/1‑148 (MQ=255)                                                                                                      aaTAAAAAATTTTCAACACATTTTTTTATAAAATTTTGGTTTCCACCCGAAAAAACGAGGTAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTc                                                      <  2:183149/141‑1 (MQ=255)                                                                                                        tACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGAt                                          >  2:593251/1‑151 (MQ=255)                                                                                                         aaaaaaTTTTCAACACCCTTATCTACTCAAATTTGGCTTGCACCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGAt                                          <  1:712184/148‑1 (MQ=255)                                                                                                         aaaaaaTTTTAAACACACTTATCTCCCCGAATTTGGCTTGCACCCGAAAAACCCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGAt                                          <  1:564115/148‑1 (MQ=255)                                                                                                         aCAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGAtt                                         >  1:200318/1‑151 (MQ=255)                                                                                                                    aaCACTCTTATCTACTCGATTTTGGCTTGCATCCGAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGtt                                 <  2:618684/148‑1 (MQ=255)                                                                                                                        cacTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTa                           >  1:705664/1‑150 (MQ=255)                                                                                                                        cacTTATCTACTCAATTTTGGCTTGCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACtt                            <  1:303179/149‑1 (MQ=255)                                                                                                                           ttATCTACTCGATTTTGGCTTGCACCCGAAAAACCCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTa                           <  1:54122/147‑1 (MQ=255)                                                                                                                             aTCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATAtt                      >  1:35392/1‑150 (MQ=255)                                                                                                                               cTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTAc                    >  1:430518/1‑150 (MQ=255)                                                                                                                                  ctcaattttGGCTTGCATCCACAAAAACAAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTa                     <  1:663175/140‑1 (MQ=255)                                                                                                                                          tgtcTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATAtt         <  2:635196/147‑1 (MQ=255)                                                                                                                                                 cATCCGAAAAAACCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGttt  <  2:186645/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                AGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTT  >  NC_000913/3665552‑3665845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑