Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,845,823	0	G	T	47.4%	53.5 / 13.5	39	R449S (CGC→AGC)	uhpT	hexose phosphate transporter
Reads supporting (aligned to +/- strand):  ref base G (17/3);  new base T (0/18);  total (17/22)
Fisher's exact test for biased strand distribution p-value = 4.02e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGGGGCTATTTGATGGCGAGAAGTTTGCCTTCACTACGCTGGAAGTCACGGAATAATAAAAAAAGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATACCGGCGTCCCATCGGCAATCATTCCCAGACCTAACTT  >  NC_000913/3845674‑3845958                                                                                                                                                           |                                                                                                                                         cAGGGGCTATTTGATGGCGAGAAGTTTGCCTTCACTACGCTGGAAGTCACGGAATAATAAAAAAAGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑Gt                                                                                                                                         <  1:770387/151‑1 (MQ=255) cAGGGGCTATTTGATGGCGAGAAGTTTGCCTTCACTACGCTGGAAGTCACGGAATAATAAAAAAAGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑Gt                                                                                                                                         <  1:659612/151‑1 (MQ=255)       cTATTTGATGGCGAGAAGTTTGCCTTCACTACGCTGGAAGTCACGGAATAATAAAAAAAGCCC‑GCCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTcc                                                                                                                                   >  2:17529/1‑151 (MQ=255)         aTTTGATGGCGAGAAGTTTGCCTTCACTACGCTGGAAGTCACGGAATAATAAAAAAAGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAt                                                                                                                                 >  1:811576/1‑151 (MQ=255)           ttGATGGCGAGAAGTTTGCCTTCACTACGCTGGAAGTCACGGAATAATAAAAAAAGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAt‑t                                                                                                                               >  1:790736/1‑150 (MQ=255)                    agaAGTTTGCCTTCACTACGCTGGAAGTCACGGAATAATAAAAAAAGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACt                                                                                                                      >  1:72923/1‑150 (MQ=255)                       aGTTTGCCTTCACTACGCTGGAAGTCACGGAATAATAAAAAAAGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCg                                                                                                                  >  2:30699/1‑151 (MQ=255)                             ccTTCACTCCGAGGAAATCCACGAAAAAAAAAAAAACCCCC‑GGCGTCAGGCGGG‑AAAAAAGCCACCATTTTTTTTTATC‑CCTCTGTCAACTGCTTATTTTTTTCCCCGG‑GGCGTTTTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCa                                                                                                               <  2:453659/148‑1 (MQ=255)                                 cACTACGCGGAAAGCCCCGAAATAATAAAAAAACCCC‑GGCGTCATGCCGG‑GAAAAAGTCCCCATTTACTTTTATG‑CCACTGTCACCTGCTAATTTTTTTTCCCGC‑GGGGTTTTTGGC‑TTTCTTCCAT‑TACCGCCACTATCGCCATCAgg                                                                                                          <  2:55212/149‑1 (MQ=255)                                          gaaaGTCACGAAAAAAAAAAAAAACCCC‑GGCGTCATGCCGG‑GAAAAAGTCCCCATTTCCTTTTATG‑CCACTGTCAACTGCTGATTTTTTTTCTCGC‑GGCGTTTTTTGC‑TTTCTCCCTT‑TACCGCCACTATCGCCATCAGGCAGATACaa                                                                                                 <  1:654583/147‑1 (MQ=255)                                           gAAGTCACGGAATAATAAAAAAAGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAAcc                                                                                               >  2:120458/1‑150 (MQ=255)                                            aaGTCACGGAATAATAAAAAAAGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCa                                                                                              >  1:749144/1‑150 (MQ=255)                                               ccaggaaataaaAAAAAACGCCC‑GTGGTCGGGCGGG‑GAAAAAGCCACCGTTTTTGTTTATC‑CCCCTTACACCTGCAGATTTTTTTCCCCGG‑GGGGGTTTTGGC‑TTTCTCCATT‑TCCCGCCACTATCGCCATCAGGCAGATACAACCAATcg                                                                                          <  2:221832/145‑1 (MQ=255)                                                   ggAATAATAAAAAAAGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCgcggc                                                                                      >  1:388355/1‑151 (MQ=255)                                                         aaaaaaaacCCCC‑GGCGTCA‑GCCGGAAAAAAAGCCCCCATTTACTTTTACC‑CCCCTGCCACCTGCTAATTTTTTTCCCCGC‑GGGGGTTTTTGT‑TTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATc                                                                                <  2:781401/149‑1 (MQ=255)                                                         aaaaaaaaaCCCCGGGCGTCACGCGGG‑ACAAAAGCCACCGGTT‑CTTTTAAGCCCCCTCTCACCTGTTAATTTTTTTTCCGGC‑GGGGTTTTTTGT‑TTTCTCCAAT‑GACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGata                                                                                  <  2:55628/148‑1 (MQ=255)                                                            aaaaaaGCCCGGGGGTCAGGCGGG‑AAAAAAGTCCCCTGTTCTGTTTACG‑CCACTTTCAACTGCTAATTTTTTTTCTGGC‑GGCGGTTTTTGT‑TTTCTCCCTT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATcc                                                                               <  1:39959/150‑1 (MQ=255)                                                               aaaGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAgcgc                                                                          >  1:119860/1‑151 (MQ=255)                                                                  gCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCgcggc                                                                       >  1:326010/1‑151 (MQ=255)                                                                   ccc‑GGCGTCATGCGGG‑GAAAAAGCCCCCATTTACTTTTATG‑CCACTGTCACCTGCTAATTTTTTTTCTCGC‑GGGGGTTTTTGC‑TTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGcgcg                                                                         <  1:833947/148‑1 (MQ=255)                                                                    cc‑GGCGTCATGCGGG‑GAAAAAGTCACCATTTGCTTTTATG‑CCCCTGTCACCTGCTAATTTTTTTTCCCGC‑GGGGGTTTTTGC‑TTTCTCCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGa                                                                     <  1:438626/151‑1 (MQ=255)                                                                       ggCGTCATGCGGG‑GCAAAAGTCCCCAGTTACTTTTATG‑CCACTGTCAACTGCTAATTTTTTTTCCCGC‑GGCGGTTTTTGC‑TTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGaa                                                                    <  1:917080/150‑1 (MQ=255)                                                                       ggCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGa                                                                     >  1:10652/1‑149 (MQ=255)                                                                                             ccccAGTTCCGTTTATC‑CCTCTTTCACCTGTTAATTTTTTTCCCCGG‑GGGGGTTTTTGC‑TTTCTTCCTT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTaa                                                <  1:100758/147‑1 (MQ=255)                                                                                               cctgttccttttATC‑CCATTGCCACCTGTTGTTTTTTTTCCCCGC‑GG‑GGGTTTTGCTTTTCTCCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGcc                                            <  1:220117/142‑1 (MQ=255)                                                                                                  gTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGa                                          >  1:877727/1‑150 (MQ=255)                                                                                                   ttACGTTTATG‑CCACTTTCACCTGCTAATTTTTTTTCCCGC‑GGGGGTTTTTGC‑TTTCTCCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGaa                                         <  1:903389/150‑1 (MQ=255)                                                                                                    tACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAAt                                        >  1:666260/1‑150 (MQ=255)                                                                                                      cGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGGATAcc                                     >  1:477976/1‑151 (MQ=255)                                                                                                        tttATC‑CCTCTGACACCGGCTAATTTTTTTTCCCGG‑GGGGGTTTTTGC‑TTTCTCCCAT‑TCCCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATa                                       <  1:791674/147‑1 (MQ=255)                                                                                                                      cAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATACCGGCGTCCCATCGGc                       >  2:711375/1‑150 (MQ=255)                                                                                                                           gctgAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATACCGGCGTCCCATCGGCAATCAt                 >  2:773228/1‑151 (MQ=255)                                                                                                                             cttaTTTTTTTCCCCCGGGCGGTTTTTGC‑TTTCCCCAAT‑ACCCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATACCGGCGTCCCATCGGCAATCa                  <  1:228728/146‑1 (MQ=255)                                                                                                                              gAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATACCGGCGTCCCATCGGCAATCATTcc              >  2:551205/1‑151 (MQ=255)                                                                                                                                tttttttcCGCGC‑GGGGTTTTTTGC‑TTTCTCCCAT‑TCCCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATACCGGCGTCCCATCGGCAATCa                  <  1:30702/144‑1 (MQ=255)                                                                                                                                           ccggggggtttttGC‑CTTCCTCCATCTCCCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATACCGGCGTCCCATCGGCAATCATTCCCAGACCTa      <  2:140263/139‑1 (MQ=255)                                                                                                                                            gggggggtttttGC‑TTTCTCCCAT‑TCCCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATACCGGCGTCCCATCGGCAATCATTCCCAGACCTAACtt  <  2:142549/142‑1 (MQ=255)                                                                                                                                              ggggatttttGC‑TTTCTTCCAT‑GCCCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATACCGGCGTCCCATCGGCAATCATTCCCAGACCTAACt   <  2:75474/141‑1 (MQ=255)                                                                                                                                                    ttttGC‑TTCCTCCCAT‑TCCCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATACCGGCGTCCCATCGGCAATCATTCCCAGACCTAACtt  <  2:500882/142‑1 (MQ=255)                                                                                                                                                           |                                                                                                                                         CAGGGGCTATTTGATGGCGAGAAGTTTGCCTTCACTACGCTGGAAGTCACGGAATAATAAAAAAAGCCC‑GGCGTCATGCCGG‑GCAAAAGTCACCAGTTACGTTTATG‑CCACTGTCAACTGCTGAATTTTTTTCTCGC‑GGCGGATTTTGC‑GTTCTTCCAT‑TACCGCCACTATCGCCATCAGGCAGATACAACCAATCGCGGCGATATCCAGCGCGGCGAAGGTGCCTGCCCAGCCGGTAAGGCCGAATACCGGCGTCCCATCGGCAATCATTCCCAGACCTAACTT  >  NC_000913/3845674‑3845958

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑