Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,665,702	0	C	A	44.1%	68.2 / 31.8	60	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
Reads supporting (aligned to +/- strand):  ref base C (28/5);  new base A (0/26);  total (28/32)
Fisher's exact test for biased strand distribution p-value = 6.86e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTAT  >  NC_000913/3665558‑3665847                                                                                                                                                 |                                                                                                                                                   gaACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAc                                                                                                                                              <  1:131732/151‑1 (MQ=255)    cGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAg                                                                                                                                           <  2:836311/151‑1 (MQ=255)       gTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑Tc                                                                                                                                       >  1:180107/1‑151 (MQ=255)              agaaACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGcc                                                                                                                                 >  1:4606/1‑150 (MQ=255)                aagcTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCCACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCAtt                                                                                                                              >  2:218595/4‑151 (MQ=255)                    ttttttATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTaaa                                                                                                                           >  1:529815/1‑150 (MQ=255)                     tttttATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAAt                                                                                                                         >  2:396637/1‑151 (MQ=255)                        ttATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑ACACCGCCATTAAAATAGc                                                                                                                      >  1:336968/1‑151 (MQ=255)                                   aaattttACTCCCTCCTCCTTGAGCACGGGGAAAAATAATAAAAGCTTGCCCTTTAACACAAAAACAAAATTTCCAACACACTTATCTCCTAAAATTGGGTTTGCCCCCGAAAAAACCAGT‑TCCCCGCCATTAAAATAGCGATATTCAc                                                                                                             <  2:785429/145‑1 (MQ=255)                                      aTTTAATGCCTCCTCCTTGAGTATCGGGAGAAATAATGAAAGAGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCAtt                                                                                                         >  2:610095/1‑150 (MQ=255)                                       tttAATGCCCCCCCCTTGACCATGGGGAAAAATAATAAAGGCGTGTCCTTGGCCACAAAAAAAAAATTTTAAACCCACTTATCAACAAAATTTTGGTTTGCACCCAAAAAAACAGGG‑TCGCCGCCATTAAAATAGCGATATTCACCATTa                                                                                                        <  2:843081/150‑1 (MQ=255)                                        ttAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAAc                                                                                                      >  1:245054/1‑151 (MQ=255)                                        ttAATCCCTCCTCCTTGAGCATCGGGAAAAATAAGAAAAGCGTACCCCTGAACACAAATAAAAAATTTCCAACACACTTATCTAATCG‑ATTTGGCTTTCCCCCGGAAAAACCCGGACCACCGCCATTAAAATAGCGATATTCACCATTaa                                                                                                       <  2:314857/150‑1 (MQ=255)                                           aTGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCAt                                                                                                   >  1:901294/1‑151 (MQ=255)                                              cctcctcctTGAGCATCGGGAGAAAAAATGAAAGCTTGTCCCTTACCACGAATAAAAATTTTACAACCCATTTATCTACTCAATTTTGGTTTGCTCCCAAAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCAt                                                                                                   <  1:795233/148‑1 (MQ=255)                                              cctccccctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAATTTTTAAACACACTTATCTACTCGAATTTGGCTTGCACCCGAAAAACCCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATgg                                                                                                 <  1:16533/150‑1 (MQ=255)                                               ctcctcctTGAGCATCGGGAGAAATAATGACAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCAACATTAACCATGGTg                                                                                               >  2:485579/1‑151 (MQ=255)                                                 cctcctTGAGCATGGGGAAAAATAATAAAGGCGTGTCCCTTGACACAAATAAAAATTTTTCAACCCCCTTATCTCCTAAATTTTGGTTTGCACCCGAAAAAACCAGT‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga                                                                                              <  1:315043/150‑1 (MQ=255)                                                 cctcctTGAGCATCGGGAAAAATAATGAAAGCGTGTCCCTTGACACGAATAAAAAATTTTAAACACACTTATCTACTCGATTTTGGCTTGAACCCGAAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                                                                                               <  1:274811/149‑1 (MQ=255)                                                  ctcctTGAGAACCGGGAAAAAAAATAAAGGCGTCCCCTTTAACAGAAAAAAAAAATTTCCAACACACTTATCTACTAAAATTTGCTTTCCACCCGAAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag                                                                                             <  1:311285/150‑1 (MQ=255)                                                    cctTGAGCATCGGGAAAAATAATAAAGGCGTGTCCCTGGACACAAATAAAAAATTTCAAACACACTTATCTACTCAATTTTGGCTTCCACCCGAAAAACCCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgaga                                                                                            <  1:295925/149‑1 (MQ=255)                                                      tggAGCATCGGGAAAAATAATGAAAGCGTGTCCGTGGACACAAATAAAAAATTTTCAACACTCTTATCTACTAAATTTGGGCTTGCATCCGAAAAAACCGGG‑AGACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgaga                                                                                            <  2:503034/145‑1 (MQ=255)                                                       tGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatat                                                                                        >  1:841855/1‑150 (MQ=255)                                                            atggggAAAAATAATGAAAGCGTGTCCCTTGACACGAATAAAAAATTTTCAACACACTTATCTCCTCAAATTTGGCTTGCATCCGAAAAAACCAGG‑ACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAata                                                                                         <  1:605441/141‑1 (MQ=255)                                                            aTCGGGAAAAAAAAGGAAAGCGTTCCCTTTAACACAAATAAAAATTTTTAAACCCACTTTTCTCCGCGAATTTGGTTTGCACCCGAAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatatat                                                                                      <  1:363964/147‑1 (MQ=255)                                                                  agaAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTg                                                                            >  1:558184/1‑151 (MQ=255)                                                                  aaaaaTAATGAAAGCGTGTCCCTTGACACGAATAAAAAATTTTAAACACACTTATCTCCTCGATTTTGGCTTGCACCCGAAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtt                                                                             <  1:295150/148‑1 (MQ=255)                                                                     aataatGAAAGCGTTTCCCTTGACACAAATACAAAATTTTCAACACACTTATCTACTCAATTTTGGTTTCCACCCGAAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCAt                                                                         <  2:701699/151‑1 (MQ=255)                                                                     aataatGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCAt                                                                         >  1:698542/1‑151 (MQ=255)                                                                      ataatGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCAt                                                                         >  2:251439/1‑150 (MQ=255)                                                                       taatGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc                                                                       >  1:685814/1‑151 (MQ=255)                                                                             aaGCGTTTCCCTTGACACAAATACAAAATTTTCAACACATTTATCTACTCGATTTTGGCTTCCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAtt                                                                 <  1:348152/151‑1 (MQ=255)                                                                                        ttGACACAAATAAAAAATTTTAAACCCACTTATCTACTCGATTTTGGCTCGCATCCACAAAAACCAGG‑TAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTc                                                        <  1:829030/149‑1 (MQ=255)                                                                                          gaaacaaaTAAAAAATTTCCAACACCCTTATCTACTCAAATTTGTTTTGCATCCAAAAAAACCGGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCa                                                     <  2:354569/144‑1 (MQ=255)                                                                                           acacGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATg                                                   >  1:430443/1‑151 (MQ=255)                                                                                              caaaTAAAAAATTTTCAACACACTTATCTACTCAAATTTGGCTTCCCCCCGAAAAAACGAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTa                                                 <  2:276188/148‑1 (MQ=255)                                                                                              cGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGt                                                  >  1:331640/1‑149 (MQ=255)                                                                                               gAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTACCCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGt                                               >  2:222999/1‑151 (MQ=255)                                                                                                aaTAAAAAATTTTCAACACACTTATCTACTCGATTTTGGCTTGCATCCGAAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAg                                                <  1:433489/149‑1 (MQ=255)                                                                                                aaTAAAAAATTTACAACACCCTTTTCGACGCAATTTTGTTTCGCA‑CCCAAAAAACCTGGCAAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATg                                                   <  2:647846/146‑1 (MQ=255)                                                                                                   aCAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGAtt                                           >  1:66999/1‑151 (MQ=255)                                                                                                   aCAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGAtt                                           >  1:288629/1‑151 (MQ=255)                                                                                                              acctcacTTTTCTACTCGAATTTGGTTTGCAACAACAAAACCAAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGATGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTg                                  <  2:636410/145‑1 (MQ=255)                                                                                                                  cccTTATCTACTCAATTTTGGCTTGCACCCGAAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTa                             <  1:109429/148‑1 (MQ=255)                                                                                                                     ttATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat                         >  1:218346/1‑151 (MQ=255)                                                                                                                      tATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATAtt                        >  1:852545/1‑151 (MQ=255)                                                                                                                        tCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTAc                      >  1:587041/1‑151 (MQ=255)                                                                                                                          tACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAt                    >  2:170511/1‑151 (MQ=255)                                                                                                                           aCTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAt                    >  1:894612/1‑150 (MQ=255)                                                                                                                           aCTCAAATTTGGCTTGCACCCAAAAAAACCAGG‑TAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTAc                      <  2:76374/148‑1 (MQ=255)                                                                                                                            ctaaaaTTTGGCTTGCCCCCGAAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACa                     <  2:591129/144‑1 (MQ=255)                                                                                                                              cGATTTTGGTTTGCACCCGAAAAAGCCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATaaa                 <  1:779499/150‑1 (MQ=255)                                                                                                                              cGAATTTGGCTTGCATCCGAAAAAACCAGT‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAAc                <  1:223788/151‑1 (MQ=255)                                                                                                                               gAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAAc                >  2:403064/1‑150 (MQ=255)                                                                                                                                 ttttGGCTTCCACCCAAAAAAACCGGT‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATaa                  <  2:180047/145‑1 (MQ=255)                                                                                                                                 aTTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACat              >  2:253975/1‑150 (MQ=255)                                                                                                                                     ggtttGCACCCGAAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTa          <  1:357937/147‑1 (MQ=255)                                                                                                                                      gtttacacccGAAAAAACCGGC‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACt        <  2:619257/143‑1 (MQ=255)                                                                                                                                              ccGCAAAAACCATG‑GCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCACATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTttat  >  2:881562/1‑149 (MQ=255)                                                                                                                                              ccGAAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTttat  <  1:765345/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                   GAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGG‑TCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTAT  >  NC_000913/3665558‑3665847

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑