Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,595,044	0	T	A	45.2%	40.8 / 21.0	42	Y146F (TAC→TTC)	livM	branched‑chain amino acid ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base T (17/6);  new base A (0/19);  total (17/25)
Fisher's exact test for biased strand distribution p-value = 4.85e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCCAGATAGTCACCGCGCAAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCCGCGTGAAACCATAAACGGCCACGCCACCGCAAGC  >  NC_000913/3594896‑3595187                                                                                                                                                         |                                                                                                                                                cGCCAGATAGTCCCCGCGCAAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTaa                                                                                                                                               <  2:145593/151‑1 (MQ=255)       aTAGTCACCGCGCAAACGCAGCCCCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAAccg                                                                                                                                         <  2:470280/151‑1 (MQ=255)       aTAGTCACCGCGCAAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAAccg                                                                                                                                         >  1:866369/1‑151 (MQ=255)       aTAGTCACCGCGCAAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAAc                                                                                                                                           <  2:828829/149‑1 (MQ=255)        tAGTCCCCGCGCAAACGCGTCACCGGAAATCCGGGCAGAACCCCCGCCGCCGCTGCCATTAATCCAGAAATC‑GTGTGGCAGGTCC‑AGAAGCCCAA‑GCCGAAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAAc                                                                                                                                           <  2:248483/148‑1 (MQ=255)        tAGTCACCGCGCAAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAAccgc                                                                                                                                        >  1:255781/1‑151 (MQ=255)                            cccgggAAACCCGGGGAGGACGCCCGCCGCCTCTGCTATAAACCCAGCACTC‑GGGGGGCGGTTCA‑AGAAGCCAAA‑GCCAAAATAGTGATTGAGCAGCAAAAAAGTGTAA‑GCGCCGATGGCGAAAAAACCGCCGTACCccagcacca                                                                                                                         <  2:861591/142‑1 (MQ=255)                            cacccaaacccgcaGCGGGGAGCCCCCCGCCGCGGCGTCTAACCCAGCAACC‑GGACCGC‑GCTCCAAGAGCCCCAA‑GCGGTAAGAGGAATTGCGCGGCTCAAAAGTAAAA‑CCGCGGAGGCCGAAAAAACCGCCGTACCccagcaccagca                                                                                                                      <  2:663431/136‑1 (MQ=255)                                        gAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGAcc                                                                                                         >  1:622272/1‑150 (MQ=255)                                           cAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACcaac                                                                                                      >  1:320473/1‑150 (MQ=255)                                               agcccccccGCCGCTCCCA‑TAACCCCACAAGC‑GGGAGGGCGGTCC‑CGAAGCCCAAGGCCTAAATAGTGATGGAGCAGCGAAAAAGTGAAA‑GCCCCGATGGCAAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACcaaca                                                                                                     <  2:39706/144‑1 (MQ=255)                                                  cccGCCGCCGC‑GGCAATAAACCAACAAACGGGCAGGGGGGCCA‑AGAGCCCAAA‑GCCGTAATAGTGATTGAGCAGCGCAAAATTGAAA‑GCGCCGATGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCAc                                                                                                <  1:253595/149‑1 (MQ=255)                                                      ccgccgcTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGATc                                                                                            >  1:939711/1‑149 (MQ=255)                                                      cccccccTGCCATAAACCCACAAACC‑GGCAGGCGGGTCA‑AGAACCCCAA‑GCCGTAATAGTGATGGAGCAGCGCAAAAGTGTAA‑GCCCCGATGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCa                                                                                           <  1:222035/144‑1 (MQ=255)                                                          cgcTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCg                                                                                      >  2:64048/1‑151 (MQ=255)                                                           gcTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCg                                                                                      >  2:170429/1‑150 (MQ=255)                                                            cTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCg                                                                                      >  1:25079/1‑149 (MQ=255)                                                                     aacccgccaacgggcaggca‑GTCC‑AAGAGCCCAAGGCCGTAATAGTAATGGGGCAGCGAAAAAG‑GTAAGGCGCGGATGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAgg                                                                             <  2:476229/138‑1 (MQ=255)                                                                     aacccagaaacgggcaggcgGGTCC‑AAAAGCCAAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGAAA‑GCGCCGAGGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGa                                                                            <  1:920011/139‑1 (MQ=255)                                                                            aaTC‑GGCGGGCAGGCCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCCCCGATGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAg                                                                    <  1:395247/151‑1 (MQ=255)                                                                            aaTC‑GGCAGGCAGGACC‑AGAAGCCCAA‑GCCGGAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATg                                                                       >  2:604056/1‑148 (MQ=255)                                                                                    aggcaggTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATgg                                                             >  1:925774/1‑151 (MQ=255)                                                                                        gcagggcaaaaacccAAGGCCGTAAAAAGGTTTGAGCACCAAAAAAGTTTAA‑GCCCCGATGGTGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTc                                                           <  1:73910/139‑1 (MQ=255)                                                                                         ggccc‑AGAAGCCCGA‑GCCGAAATGGGGAGTGGGCGGCGCAAGAGTGTAA‑GCGCCGATGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAg                                                         <  2:213431/147‑1 (MQ=255)                                                                                           gccaaaaggCCAAA‑GCCTTAATAGTGATTGAGCAGCCAAAAAGTGAAA‑GCGCCAAGGGCAAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCa                                                                <  1:513176/134‑1 (MQ=255)                                                                                                 aaGCCAAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGt                                                      <  1:666694/146‑1 (MQ=255)                                                                                                  acccaaa‑GCCGAAATAGTGATGGAGCAGCACAAAAGTTGAA‑GCGCCGATGGCGAAAAACCCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCa                                                  <  2:675115/144‑1 (MQ=255)                                                                                                    ccaaa‑GCCGTAATATTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTgg                                                    <  1:155479/142‑1 (MQ=255)                                                                                                      cAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAatat                                              >  2:494378/1‑149 (MQ=255)                                                                                                       aa‑GCCGTAATAGTGATGGTGCAGCGAAAAAGTGTAA‑GCGCCGAGGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATct                                            <  2:465468/150‑2 (MQ=255)                                                                                                              tAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTcc                                     >  2:510133/1‑151 (MQ=255)                                                                                                               aaTAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGt                                       <  1:329389/148‑1 (MQ=255)                                                                                                                atatggATGGAGCAGCGCAAAAGTGTAA‑GCGCCGAGGGCGAAAAACCCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCcg                                   <  2:121308/146‑1 (MQ=255)                                                                                                                       ttGAGCAGCGAAAAAGTGTAA‑GCGCCGATGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCCGCGTGa                              <  1:527412/149‑1 (MQ=255)                                                                                                                        tGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCCGCGTGAAAc                           >  2:347699/1‑151 (MQ=255)                                                                                                                        gggccacccaaaaaGTGTAA‑GCGCCGATGGGGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCCGCGTGa                              <  2:923411/138‑1 (MQ=255)                                                                                                                            caccgcAAAAGTGAAA‑GCGCCGAGGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCCGCGTGAACCCAt                        <  2:366487/147‑1 (MQ=255)                                                                                                                             agcGAAAAAGTGTAA‑GCGCCGATGGCGAAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCCGCGTGAAACCATa                       <  1:411901/150‑1 (MQ=255)                                                                                                                                       tgtAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCCGCGTGAAACCATAAACGgccacgc            >  2:613500/1‑151 (MQ=255)                                                                                                                                          aa‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCCGCGTGAAACCATAAACGgccacgccac         >  2:722053/1‑151 (MQ=255)                                                                                                                                                 cGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCCGCGTGAAACCATAAACGGCCACGCCACCGCa     >  1:782557/1‑149 (MQ=255)                                                                                                                                                  gATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCCGCGTGAAACCATAAACGGCCACGCCACCGCAAGc  >  1:784706/1‑151 (MQ=255)                                                                                                                                                         |                                                                                                                                                CGCCAGATAGTCACCGCGCAAACGCAGCACCGGAAAACCGAGCAGGAAGCCCGCCGCCGCTGCCATTAATCCAGCAATC‑GGCAGGCAGGTCC‑AGAAGCCCAA‑GCCGTAATAGTGATTGAGCAGCGCAAAAGTGTAA‑GCGCCGATGGCGTAAAAACCGCCGTACCCCAGCACCAGCAGACCAGAAAGACCAACAACCACGTTCAGCCCGAGACCGAGGATAATGTAGATCATGGTCAGGGTGGCAATATCCACCGTCCCGCGTGAAACCATAAACGGCCACGCCACCGCAAGC  >  NC_000913/3594896‑3595187

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑