Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,665,698	0	T	C	53.1%	28.1 / 72.8	51	D38G (GAT→GGT)	gadX	acid resistance regulon transcriptional activator; autoactivator
Reads supporting (aligned to +/- strand):  ref base T (18/5);  new base C (0/26);  total (18/33)
Fisher's exact test for biased strand distribution p-value = 2.91e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-09

CTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTAC  >  NC_000913/3665548‑3665840                                                                                                                                                         |                                                                                                                                               ctacAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCAt                                                                                                                                                >  2:217240/1‑151 (MQ=255)      gTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCa                                                                                                                                           >  2:360778/1‑151 (MQ=255)      gTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCa                                                                                                                                           >  1:293412/1‑151 (MQ=255)      gTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCa                                                                                                                                           >  1:622740/1‑151 (MQ=255)      gTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCa                                                                                                                                           >  1:583162/1‑151 (MQ=255)            aaCGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAAcc                                                                                                                                     <  2:602088/151‑1 (MQ=255)                  tAATGAAGAAGCTTTTTTATGTGCATGAAGATTTAATTCCTCCTCCTTGAGCATCGGGAGAAATAATG‑AAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTc                                                                                                                                <  2:97755/149‑1 (MQ=255)                                               gATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt                                                                                                  >  1:503681/1‑151 (MQ=255)                                                aTTTAATGCCTCCTCCTTGCGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTa                                                                                                 >  2:639682/1‑151 (MQ=255)                                                aTTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTa                                                                                                 >  1:196163/1‑151 (MQ=255)                                                   tAATCCCCCCTCCTTGACACTGGGAAAAAATAATAAAGGCGTTTCCTTGAAAAAGAATAAAAAATTTTCAACCCATTTTTTTCCTCAAT‑TTTGG‑CTTGCACCCAAAAAAACCAGTTCCCCGCCATTAAAATAGCGATATTCACCATTAAcc                                                                                              <  2:579664/151‑1 (MQ=255)                                                       gCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATgg                                                                                          >  1:460741/1‑151 (MQ=255)                                                         ctccccttagAGCATGGAGAAAAAAAATAAAAGCGTGCCCCTTGACACGAATAAAAAATTTACAACCCCCTTATCTCCT‑AAA‑TTTGGTATTGCACCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                                                                                        <  1:583170/142‑1 (MQ=255)                                                            ctcctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgaga                                                                                     >  2:78739/1‑151 (MQ=255)                                                             ccctgaagcacggggAAAAAAAATAAAGGCTTCTCCTTTGACACAAAAAAAAAATTTTCAACACCTTTATCTACACAAT‑TTGGG‑TTTCCACACGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa                                                                                    <  1:550789/139‑1 (MQ=255)                                                              cctTGAGCATCGGGAAAAATAATGAAAGCGTGTCCCTTGCCACGAATACAAATTTTCCAACACACTTATCTCCTCAAT‑TTTGG‑TTTGCACCCCAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat                                                                                   <  1:609703/151‑1 (MQ=255)                                                                tggagctgggggAAAAAAAATGAAGGGGTGCCCCTTACCACAAATAAAAAATTTTCAACCCCTTTTTCTTCCCGAT‑TTTGG‑CTTGCAACCGAAAAACCCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatat                                                                                 <  2:109459/142‑1 (MQ=255)                                                                  gAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatatat                                                                               >  1:566040/1‑151 (MQ=255)                                                                     cATCGGGAAAAAAAAAAAAAGCGTTTCCCTTGACACAAATAAAAAATTTTCACCACCCTTATCACCTAAAA‑TTTGG‑CTTGCACCCGAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAtt                                                                              <  2:557348/149‑1 (MQ=255)                                                                       tgggaaaaaaTAAAGAAAGCGTTTCCTTTAACACAAAAAAAAATTTTTCAACCAACTTATCTTCTGAAA‑TTTGG‑CTTGCACCCGAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATg                                                                          <  2:196215/144‑1 (MQ=255)                                                                        cGGGAAAAATAATGAAAGCGTCTCCCTTACCACAAATAAAAAATTTTCAACACCCTTATCTACTCAAA‑TTTGG‑CTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGt                                                                         <  2:467856/151‑1 (MQ=255)                                                                        cGGGAAAAAAAATGAAAGCGTTCCCCTTGACAAAAAAAAAAAATTTCAAACCCCTTTATCTCCCCAAA‑TTGGG‑TTTGCCCCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGt                                                                         <  2:293516/151‑1 (MQ=255)                                                                         gggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGt                                                                         >  1:157650/1‑150 (MQ=255)                                                                          ggAGAAAAAATGAAAGCGTGTCCCTTGACACAAATAAAAATTTTCCAACACACTTATCTCCACAAT‑TTTGG‑TTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc                                                                        <  1:14556/150‑1 (MQ=255)                                                                             gaAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTg                                                                     >  1:135466/1‑150 (MQ=255)                                                                                 taatGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa                                                                 >  2:381844/1‑150 (MQ=255)                                                                                  aatGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACg                                                               >  2:597511/1‑151 (MQ=255)                                                                                            ttccctttaacacAAAAAAAAATTTTACACCCCATTTATCTCCTGGAA‑TTTGG‑CTTACACCAACAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGAc                                                      <  1:132635/141‑1 (MQ=255)                                                                                            tgtCCCTTGACAAGAATAAAAAATTTTCAACACACTTATCTACGCGAA‑TTTGG‑CTTGCACCCAAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGAc                                                      <  1:537609/150‑1 (MQ=255)                                                                                            tgtCCCTTAACAAAAAAACAAAATTTCCAACCCACTTATCTACTAGAT‑TTTGG‑TTTGCACCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGAc                                                      <  1:237605/150‑1 (MQ=255)                                                                                               cccTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAtt                                                  >  2:260803/1‑151 (MQ=255)                                                                                                 ctgaaaaaaaaTAAAAAATTTTAACCACCCTTATCTACTCAAA‑TTTGG‑TTTGAACCCAAAAAAACCGGGTAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTcc                                                <  2:138691/142‑1 (MQ=255)                                                                                                 cTTCACCCGAATAAAAAATTTAAAACCCATTTATCTACTAAAA‑TTTGG‑CTTGCATCCGCAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTcc                                                <  1:404577/151‑1 (MQ=255)                                                                                                     ccacaAATAAAAAATTTCAAACACCTTTATCAACTAAAA‑TTTGG‑CTTGCCCCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATg                                            <  2:349366/150‑1 (MQ=255)                                                                                                        caaaTACAAAATTTCCAACACCCTTATCAACAAAAT‑TTTGG‑TTTTCACCCGAAAAACCGAGGACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAg                                         <  1:54726/149‑1 (MQ=255)                                                                                                        cGAATACAAAATTTTCAACACACTTATCTACTAGAT‑TTTGT‑CTTGCACCCACAAAAACCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAg                                         <  1:192260/151‑1 (MQ=255)                                                                                                            aaaaaaaTTTACAACCCCTTTATCTA‑TCAAATTTTGG‑CTTCCCCCCGCAAAAACCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGAt                                     <  2:556487/148‑1 (MQ=255)                                                                                                                  aTTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATa                               >  1:189817/1‑151 (MQ=255)                                                                                                                         acacacTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGa                          >  2:198250/1‑149 (MQ=255)                                                                                                                           cctcTTATCTACCCAAT‑TTTGG‑CTTCCACCCGAAAAAACCGGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTa                      <  1:503190/148‑1 (MQ=255)                                                                                                                           ccctttATCTCCTGAAT‑TTTGT‑CTTCCACCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTa                      <  1:561944/147‑1 (MQ=255)                                                                                                                              cTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAata                   >  1:589996/1‑151 (MQ=255)                                                                                                                               ttttttACTCAAT‑TTGGG‑CTTTCTTCCGAAAAACCCGGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATCTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat                  <  2:406200/146‑1 (MQ=255)                                                                                                                               ttttCTACTCGAA‑TTTGC‑TTTCCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat                  <  2:212639/148‑1 (MQ=255)                                                                                                                               ttttCTACTAGAA‑TTTGT‑TTTGCCGCCAAAAAACCAAGATAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat                  <  2:317398/148‑1 (MQ=255)                                                                                                                               ttttCTACCCGAT‑TTTGG‑TTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat                  <  2:593713/148‑1 (MQ=255)                                                                                                                               tttccTACTCAAT‑TTTGG‑TTTCCATCAAAAAAAACCGGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat                  <  1:78727/147‑1 (MQ=255)                                                                                                                                     tactgaattttGG‑CTGCCACCAGAAAAAACAGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAt             <  1:101240/143‑1 (MQ=255)                                                                                                                                     cattcaattttGG‑CTTCCACCCCCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAt             <  2:293073/143‑1 (MQ=255)                                                                                                                                           attttGT‑CTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACat       <  1:601590/149‑1 (MQ=255)                                                                                                                                                 g‑CTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTAc  <  2:546321/150‑1 (MQ=255)                                                                                                                                                  gtttGCACCCAAAAAACCCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTAc  <  2:441647/148‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                               CTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAA‑TTTGG‑CTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTAC  >  NC_000913/3665548‑3665840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑