Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,601,170	0	G	C	40.8%	72.3 / 18.0	49	A306G (GCA→GGA)	ftsX	putative ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base G (19/10);  new base C (0/20);  total (19/30)
Fisher's exact test for biased strand distribution p-value = 2.03e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTT  >  NC_000913/3601020‑3601311                                                                                                                                                           |                                                                                                                                               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         >  1:885676/1‑150 (MQ=255)                                                                                                                                        gTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCa         >  2:221352/1‑150 (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)                                                                                                                                                           |                                                                                                                                               CGCTTTTATTATTCAGGCGTAAAGTGGCGTAAATGTTGTACCGTGGCAAGCCACGCTGCCACCCAGCCAATCATCGAGCATACCAGCAGCAATAGCAGGCATTCATCGAATGATAAGCCATTGATATCAAACTTCGTTCC‑GAAAA‑CC‑TG‑TGCCACTT‑CCGCAACCGCCGATGACAATCGCAGCACCAGAATTTCTGACAAAATTAATGACAACAATGCGCCAGAAAATCCCAGCAGTGCGCCACCATACAGGAACGGGCGCAGGATGAATCCATCTGTCGCACCAATCAGTT  >  NC_000913/3601020‑3601311

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: ‑