Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,601,176	0	T	C	46.8%	43.7 / 24.6	47	E304G (GAA→GGA)	ftsX	putative ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base T (18/7);  new base C (0/22);  total (18/29)
Fisher's exact test for biased strand distribution p-value = 1.07e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGTACGTTAATGG  >  NC_000913/3601028‑3601326                                                                                                                                                         |                                                                                                                                                        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)                                                                                                                                 cgtccaaaatccc‑TG‑TCCCCCTC‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGc                            <  1:393960/136‑1 (MQ=255)                                                                                                                                       aaac‑CC‑TG‑TCCCCCTC‑CCGCACCCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGtt                 <  1:80908/151‑1 (MQ=255)                                                                                                                                       aaac‑CC‑TG‑TCCCACTC‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAg                   <  2:366634/149‑1 (MQ=255)                                                                                                                                                         t‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGTACGTTAATgg  >  1:574577/1‑151 (MQ=255)                                                                                                                                                         |                                                                                                                                                        TTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTTTCTGTACGTTAATGG  >  NC_000913/3601028‑3601326

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑