Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,601,160	0	G	A	39.6%	59.0 / 24.1	51	F309F (TTC→TTT)	ftsX	putative ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base G (22/7);  new base A (0/19);  total (22/29)
Fisher's exact test for biased strand distribution p-value = 7.36e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGTATAACACGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCA  >  NC_000913/3601010‑3601304                                                                                                                                                        |                                                                                                                                                     gagTATAACACGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑g                                                                                                                                                      >  2:462891/1‑151 (MQ=255)   gTATAACACGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑Ga                                                                                                                                                     >  2:8564/1‑150 (MQ=255)    tataACACGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑Gaa                                                                                                                                                    >  1:341239/1‑150 (MQ=255)     ataACACGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATATCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑Gaaa                                                                                                                                                   <  1:1080713/150‑1 (MQ=255)         cacGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑tg                                                                                                                                            >  1:841295/1‑151 (MQ=255)           cGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑tg‑tg                                                                                                                                         <  2:114404/151‑1 (MQ=255)              ttttATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGcc                                                                                                                                       >  1:140436/1‑150 (MQ=255)               tttATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCa                                                                                                                                      <  1:708055/150‑1 (MQ=255)                   ttattCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑cc                                                                                                                                >  1:23917/1‑151 (MQ=255)                    tattCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑cc                                                                                                                                <  2:1021587/150‑1 (MQ=255)                     attCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCTCCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTTATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCg                                                                                                                               <  1:560421/150‑1 (MQ=255)                       tCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGCTAAGCCATTGATATCAAACTTCGTTCC‑TAAAA‑CC‑TG‑TGCCACTT‑CCGCa                                                                                                                             <  1:137541/150‑1 (MQ=255)                       tCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCa                                                                                                                             <  2:681667/150‑1 (MQ=255)                         aGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAAcc                                                                                                                          >  2:394028/1‑151 (MQ=255)                          ggtgTAAAGTGGCGTAAATGTTGAACAGTGGAAAGCCACGATGATACCCAGTAAATCATAGAGAATACGAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTAGTTCC‑GAAAA‑CA‑TG‑TGCCACTT‑CAGCaa                                                                                                                            >  1:237586/4‑148 (MQ=255)                                                 accgggggaaacccccGCTCCCCCCCACCAAATCACCGACAATCCCACAAAAAAAAGGAGGCATTCATCAAATAAAAAGCCTTTAATAAAAACCTTCGTCCA‑AAAAA‑CC‑GG‑CGCCCCTC‑CCGCAACCGCCGATGACAATCGCAGCACCAg                                                                                                   <  2:1049938/135‑1 (MQ=255)                                                  aCCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGa                                                                                                  >  2:17457/1‑150 (MQ=255)                                                   ccGTGGAAACCCCCGCTCCCCCCCACCCAATCAGGGAGCAACCCAGAAAAAATAGCGGGCATAAATAAAATGAAAAGCATTTAATATAAAACTCCG‑TCC‑AAAAA‑CC‑CG‑GGCCCTTTCCCCCATCCGCCGATGACAATCGCAGCACCa                                                                                                    <  2:953376/147‑1 (MQ=255)                                                     gTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAAttt                                                                                              >  2:386645/1‑151 (MQ=255)                                                             ccccgcccccccccacccaACCACCGAGCACCCCAGAAGAAAAAGCAGGCATTCATCAAATGAAAACCATTTAAAATAAACCTTCGTCCC‑AAAAC‑CC‑TG‑TCCCCCTC‑CCAAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACa                                                                                        <  2:1003441/138‑1 (MQ=255)                                                                cGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAAtt                                                                                   >  1:1076093/1‑151 (MQ=255)                                                                cGCTCCCCCACAGCCAACCATCAAAAACCCCGGCAGAAAGACCAGGCTTTCCTCAAATAAAAAGCTTTTATTATCAACCTT‑GTCCCTAAAAA‑CC‑TG‑CCCCCCTC‑CCCAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAAtt                                                                                   <  2:181610/151‑1 (MQ=255)                                                                  ccgCCACCCAGCCAATCACCGACCACCCAAACAAAAAAAACAGGAATTCATCAAATTATAAGCCATAAATATCAATCTCCGTCCA‑AAAAC‑CC‑GG‑CCCCCCTC‑CCAAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACaa                                                                                       <  2:508480/143‑1 (MQ=255)                                                                     ccccccACCAAATCACCGAGCACACCAGAAAAAATAGCAGGCTTTCATCAAATAATAAGCTATTGATAACAACCTTCGTCCA‑AAAAC‑CC‑TG‑TCCCCCTC‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAAt                                                                                <  2:98868/146‑1 (MQ=255)                                                                     ccACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATg                                                                               >  1:430519/1‑150 (MQ=255)                                                                       aCCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGac                                                                             >  1:618743/1‑150 (MQ=255)                                                                         ccagaaaaTCATCGACCACCCCAGCAAAAAGAGCAGGCTTACAGCAAATGAAAGGCCATTAATA‑CAAATCTCCTCCC‑AAAAACCC‑TG‑TCCCCCTC‑CAAAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGacaa                                                                           <  1:17070/144‑1 (MQ=255)                                                                                    cgaacaacaCCAGAAGAAATGGCAGGTTTCCATCAAATAATAACCATTTAATAACAACTTTCG‑TCC‑AAAAA‑CC‑CGTTCCCTTTT‑CCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCa                                                                 <  2:41620/141‑1 (MQ=255)                                                                                     cGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGa                                                               >  1:1018043/1‑150 (MQ=255)                                                                                         cATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATc                                                          >  1:187048/1‑151 (MQ=255)                                                                                          aaaCCAGCAAAAATAGCAGGCATTCAGCAAATAATAAGCCATTAATAACAAACTTCGTTCC‑AAAAC‑CC‑TT‑TCCCTTTC‑CCGAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGaaa                                                             <  1:408497/145‑1 (MQ=255)                                                                                             ccaacaaaaaTAGCAGCCATCCAACAAATGAAAAGCCATAAATACCAACCTTCGTCCC‑AAAAC‑CC‑TG‑CCCCACTC‑CAAAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCca                                                       <  1:740922/142‑1 (MQ=255)                                                                                             caagaagaaaTAGCAGATATTCATCAAATAATAAGCCATTGATA‑CAAACTTTCGTCC‑GAAAACCC‑TG‑TGCCTCTC‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCcag                                                      <  2:288494/143‑1 (MQ=255)                                                                                                gcaaaaaTAGCAAGCATTCAAAAAATAAAAAGCTATTGATATAAACCTTCTTCCC‑AAACC‑CC‑TG‑CGCCCCTC‑CCCAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGaa                                                              <  2:877872/135‑1 (MQ=255)                                                                                                 cagaaATAGCAGGCATTCATCGAATGATAAGCTTTTGATATCAAACTTCGTCCC‑AAAAC‑CC‑GG‑TGCCCCTC‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCcagca                                                    <  2:825723/149‑1 (MQ=255)                                                                                                                ttaatagAATAATAAGCCTTTAATATAAACCTTCTTCCC‑AAAAC‑CC‑TG‑TCCCCCTC‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGccacca                                         <  2:95351/139‑1 (MQ=255)                                                                                                                  cATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGa                                  >  2:435896/1‑150 (MQ=255)                                                                                                                  aatagAATGATAGTCCATAGATATCAACCTCCGTTCA‑AAAAC‑CC‑TG‑GCCCCCTC‑CCCCACCCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACa                                     <  1:198787/143‑1 (MQ=255)                                                                                                                       aataatAACCTATTAATAACAACCTTCGTCCC‑AAAAC‑CC‑TG‑TCCCCCTC‑CCCCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACgg                              <  2:278830/149‑1 (MQ=255)                                                                                                                       aaagaaaaGCCATTAATACAAACCTCCGTCCC‑AAAAC‑CC‑GG‑TCCCCCTC‑CCAAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATa                                       <  2:813505/134‑1 (MQ=255)                                                                                                                       aaTGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGgc                            >  2:846745/1‑151 (MQ=255)                                                                                                                             aaGCAATTAATACCAACCTTCGTCCC‑AAAAC‑CC‑TG‑TCCCCCTC‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCa                         <  2:912012/148‑1 (MQ=255)                                                                                                                                cctttaatatCAACCTTCGTCCC‑AAAAC‑CC‑TG‑TCCCCCTT‑CCCAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGAt                     <  2:475162/143‑1 (MQ=255)                                                                                                                                ccATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATg                    >  2:548752/1‑150 (MQ=255)                                                                                                                                      aaaaacaatcttcttCC‑CAAAA‑CCTTC‑TCCCCCTC‑CCACATCCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGTATGAATCCa              <  1:974691/138‑1 (MQ=255)                                                                                                                                       tatCAAACTTCGCTAC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGAGACTCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATAAAGGAACGAGCGCAGCATCACTCCAt             >  1:608854/1‑150 (MQ=255)                                                                                                                                         tCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTg          >  2:571560/1‑151 (MQ=255)                                                                                                                                           aaccttcttCCC‑AAAAC‑CC‑TG‑TCCCACTC‑CCCCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCt           <  2:471815/145‑1 (MQ=255)                                                                                                                                            aaCTTTCTTCC‑CAAAACCC‑TG‑TCCCCCTC‑CCCAAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTc        <  2:204559/151‑1 (MQ=255)                                                                                                                                               ttCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCAc    >  1:384758/1‑151 (MQ=255)                                                                                                                                                  gTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCa  >  2:221352/1‑150 (MQ=255)                                                                                                                                                  gTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCa  >  1:885676/1‑150 (MQ=255)                                                                                                                                                        |                                                                                                                                                     GAGTATAACACGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCA  >  NC_000913/3601010‑3601304

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑