Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,585,058	0	T	C	42.9%	66.4 / 12.7	49	intergenic (+15/+23)	yrhB/ggt	stable heat shock chaperone/gamma‑glutamyltranspeptidase
Reads supporting (aligned to +/- strand):  ref base T (24/4);  new base C (0/21);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 3.76e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCTTAGCTGGTAACGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCTTTT  >  NC_000913/3584912‑3585207                                                                                                                                                    |                                                                                                                                                      cgcTTAGCTGGTAACGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTccc                                                                                                                                                    >  2:440960/1‑150 (MQ=255) cgcTTAGCTGGTAACGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTccc                                                                                                                                                    >  2:545952/1‑150 (MQ=255)       gCTGGTAACGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAaga                                                                                                                                             <  1:716224/151‑1 (MQ=255)            tAACGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCACTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGACTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGcc                                                                                                                                        >  2:480663/1‑151 (MQ=255)              aCGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGc                                                                                                                                      >  1:519089/1‑151 (MQ=255)                  aCCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAAc                                                                                                                                  >  1:9086/1‑151 (MQ=255)                       ttattaTTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCtt                                                                                                                               >  1:198301/1‑149 (MQ=255)                       ttattaTTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTa                                                                                                                              <  1:57022/150‑1 (MQ=255)                         attattGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTa                                                                                                                           <  1:653754/151‑1 (MQ=255)                            attGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTAccc                                                                                                                        >  2:535849/1‑151 (MQ=255)                            attGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTAccc                                                                                                                        >  1:28456/1‑151 (MQ=255)                                      aCAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTaa                                                                                                               >  1:749211/1‑150 (MQ=255)                                                   tcattcTCGGGAAACGACAAAACCGCTGGAAGAATATCTACAGGATTAAAAAAAAAAAAAGGCTCCCTTCGGCTTCCCCT‑AAAAAAATCCCCCTCTCCCCACGAAGAGGGCCTCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAg                                                                                                  <  1:829623/150‑1 (MQ=255)                                                        ctctGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCggg                                                                                            >  2:637810/1‑151 (MQ=255)                                                            gggAACGGAAAACCCGCGGAAAAAATATAAACGGGATGACAAAAAAAAAAAGGCTCCCTTGGGCTTCCCCT‑GACAAAATCCCCCTCTCCCCGCGAAGGGGGCCGCTACCCTTGTTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCg                                                                                         <  2:714716/150‑1 (MQ=255)                                                            gggAACGGAAAAACCGTTGGAAAAATTTTTAAGGGATTAGAAAAAAAAAAGGGCTACCTTGGTTTTGCCCT‑GAAAAAATAGCCCTCTCCCCACGAAGAGGCCCGATACCCTTATGACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCg                                                                                         <  1:775689/150‑1 (MQ=255)                                                                  ggaaaacCCGCGGAAAGAATATCTACAGGATTACAAAAAAAAAAGGGCTCCCTTCGGCTTCCCCT‑AAAAAAATAGCCCTCTCCCCACGAGGGGGCCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATgc                                                                                    <  1:484629/146‑1 (MQ=255)                                                                  ggCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATgcgc                                                                                  >  2:116504/1‑151 (MQ=255)                                                                     aaaaCCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGt                                                                               >  1:374522/1‑151 (MQ=255)                                                                     aaaaCCGCTGAAAGAATATCTACAGTATTAAGAAAAAAAAAGGGCTCCCTTCGCCTTCCCCT‑GAAAAAATACCCCTCTCCCCACGAAGAGGGCCGTTAACCTAATTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGAt                                                                                      <  2:319424/144‑1 (MQ=255)                                                                        cccGCTGAAAAAATATCTACAGATTTACAAAAAAAAAAGGGCCCCCTGCGCCTTGCCCT‑AAAAAAATCCCCCTCTCCCCACGAAGAGGCCCGCTACCTTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACa                                                                            <  2:738630/150‑1 (MQ=255)                                                                           ggtgaaagaaTATCTAAAGTATAACGAAAAAAAAAAGCCTCCCTTCGGCTGCCCCT‑GAAAAAATCCCCCTCTCCCCACAAAGAGGGCCGCTAACCTTAGCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACt                                                                         <  2:630723/146‑1 (MQ=255)                                                                           gCTGGAAGAATATCTACAGTATTAAAAAAAAAAAAAGGCTCCCTTCGGCTCCCCCT‑AAAAAAATCGCCCTCTCCCCAAGAAGGGGGCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACaa                                                                           <  2:800789/149‑1 (MQ=255)                                                                             tGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCCTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTc                                                                        >  2:593598/1‑150 (MQ=255)                                                                              gaaataaTCTCTACAGGATTACAAAAAAAAAAAGGCTCCCTTCGGCTTCCCCT‑AACAAAATACCCCTCTCCCCCAGAAGGGGGCCGCTACCATTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTc                                                                        <  2:585031/144‑1 (MQ=255)                                                                                aaaaaTATCTACAGAATTACAAAAAAAAAAAGGCTCCCTTCGGCTTCCCCT‑GAAAAAATACCCCTCTCCCCACGAAGAGGCCCGCAACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCAcc                                                                     <  1:510941/147‑1 (MQ=255)                                                                                aaaaaTATCTACAGAATAACAAAAAAAAAAAGGCTCCCTTCGGCTTCCCCT‑AAAAAAATACCCCTCTCCCCACGAAGAGGCCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCAc                                                                      <  1:158868/146‑1 (MQ=255)                                                                                 agaaTATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGt                                                                   >  2:158250/1‑151 (MQ=255)                                                                                      atCTACAGAATTACAAAAAAAAAAAGGCTACCTTCGGCTTCCCCT‑AAAAAAACACCCCTCTCCCCACGAAGAGGGCCGCTAACCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCg                                                                <  1:195825/149‑1 (MQ=255)                                                                                            aGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAAcc                                                        >  2:108521/1‑151 (MQ=255)                                                                                             gaatcacaaaaaaaaaaaGTCTCCCTCCGGCTTCCCAA‑AACAAAAGCGCCTTCCCCCCAGCAAGAGGCCCCCTACCCTAAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCa                                                       <  2:303397/143‑1 (MQ=255)                                                                                                     aaaaaaaaAGGGCTCCCTGCGTTTCCCCCA‑GAAAAAACCGCCCTCTCCCCACGAGGAGGGCCTCTACCCTTATTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAAc                                                         <  1:330948/141‑1 (MQ=255)                                                                                                      aaaaaaaaaGGCCCCCCTCGGCCTTCCCTAAAAAAAATCCCCCTCCTCCCACGAGGAGGCCCGTAACCCTAAGCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCtt                                               <  2:51343/148‑1 (MQ=255)                                                                                                        tAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTtgt                                            >  1:39527/1‑151 (MQ=255)                                                                                                         aaaaaaGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTtgtg                                           >  2:801274/1‑151 (MQ=255)                                                                                                          aaaaaGCCTCCCTTGGGCTTCCCCG‑AAAAAAATAGCCCTCTCCCCACGAAGGGGGCCCCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTgtgt                                          <  1:804968/151‑1 (MQ=255)                                                                                                             aaGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACt                                       >  1:342564/1‑151 (MQ=255)                                                                                                                   aCCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCAt                                 >  2:586839/1‑151 (MQ=255)                                                                                                                    ccTTCGGCTTCCCCT‑AAAAAAATCCCCCTCTCCCCACGAAGGGGCCCGCTACCTTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATc                                <  1:546124/151‑1 (MQ=255)                                                                                                                           cTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCtt                         >  2:19467/1‑151 (MQ=255)                                                                                                                             tGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTc                       >  1:486502/1‑151 (MQ=255)                                                                                                                               cccT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTc                       >  1:444596/1‑149 (MQ=255)                                                                                                                               cccT‑GAAAAAATACCCCTCTCCCCAGGAAGGGGCCCCCAACCCTTAGACCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAg                     <  1:217065/151‑1 (MQ=255)                                                                                                                               cccT‑GAAAAAATACCCCTCTCCCCACGAAGAGGGCCGCTAACCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCttt                        <  1:528722/148‑1 (MQ=255)                                                                                                                               cccT‑AAAAAAATGCCCCTCTCCCCACGAAGAGGCCCCATACCTTTAGCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGc                              <  1:737328/142‑1 (MQ=255)                                                                                                                               cccA‑GACAAAACCGCCCTCTCCCCACGAAGAGGCCCGCTACCCTAACTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCctc                           <  2:518196/145‑1 (MQ=255)                                                                                                                                       aaaaTACCCCTCTCCCCACGAAGAGGGCCCCAACCCTTCGCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAgcg                   <  2:414122/146‑1 (MQ=255)                                                                                                                                         aaTAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACttt            >  2:421980/1‑151 (MQ=255)                                                                                                                                                 tctTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCtt    >  2:277486/1‑151 (MQ=255)                                                                                                                                                   ttCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCtttt  >  2:412591/1‑151 (MQ=255)                                                                                                                                                   ttCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCtttt  >  2:341222/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                                      CGCTTAGCTGGTAACGCACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAACCGCTGGAAGAATATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCT‑GACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCTTTT  >  NC_000913/3584912‑3585207

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑