Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,676,106	0	C	A	39.6%	70.8 / 25.4	53	L240F (TTG→TTT)	yphD	putative sugar ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base C (24/8);  new base A (1/20);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 4.63e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01

CGTAATCACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGAT  >  NC_000913/2675959‑2676252                                                                                                                                                     |                                                                                                                                                    cGTAATCACCAGCACACCAAGCAAGGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACaaa                                                                                                                                                  <  2:938083/151‑1 (MQ=255)    aaTCACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAt                                                                                                                                                >  2:661408/1‑150 (MQ=255)    aaTCACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑g                                                                                                                                              <  1:729385/151‑1 (MQ=255)         ccAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGt                                                                                                                                         <  2:634232/151‑1 (MQ=255)           aGCACCCCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCa                                                                                                                                       <  2:153836/151‑1 (MQ=255)              acacCAAGCAATGTACCGTACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCAccg                                                                                                                                    >  1:391767/1‑151 (MQ=255)              acacCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCAccg                                                                                                                                    >  2:512842/1‑151 (MQ=255)                  cAAGCAATTTCCCGAACAGGGACCCGCGCCCGCCGGAACGTGCCGTCCCGCCGCCCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTCCCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCAccgccg                                                                                                                                 <  2:504357/150‑1 (MQ=255)                  cAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACcgccgc                                                                                                                                >  2:873255/1‑151 (MQ=255)                   aaGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCt                                                                                                                               >  1:842398/1‑151 (MQ=255)                    aGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCt                                                                                                                               >  2:759373/1‑150 (MQ=255)                       aaTGTACCGAACAGGGAACCGCGACCGCCGGACAGTGCCGTACCGCCGGCCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCCCGCCGCCAACAAAAT‑GCCGGTCACcgccgcca                                                                                                                              >  2:363867/1‑146 (MQ=255)                        aTGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCtaata                                                                                                                           >  1:696296/1‑150 (MQ=255)                              cGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCg                                                                                                                     >  1:398973/1‑150 (MQ=255)                                 aaaGGGAACCGCGAGCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGTCGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTCCCACACCC‑GAGGCGCGCCGCCAAAAACAT‑GCCGGTCACCGCCGCTCATAATCCCGaa                                                                                                                   >  2:714070/3‑149 (MQ=255)                                   aGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTCATAATCCCGAAAggg                                                                                                               >  1:82640/1‑151 (MQ=255)                                        aCCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaa                                                                                                            >  1:240345/1‑149 (MQ=255)                                         cggcgcCCGCCGGAAAGGGCCGTCCCGCCGCCCCCGCCCGCGGCGATGCCGTCAAACCCCAGCCCGTTGGCGGCCCCGGTGTTCCCAGAACC‑GAGGCGCCCCGCAAAAAAAGT‑GCCGGGCACCGCCGCTAATAATCCCGAAAGGGTaa                                                                                                            <  2:433200/146‑1 (MQ=255)                                          cgcgACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAACAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTaa                                                                                                            >  2:724721/1‑147 (MQ=255)                                            cgACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATa                                                                                                       >  1:57425/1‑150 (MQ=255)                                               ccgccgAAAAGGCCCGTCCCGCCGCCCCCGCCCGCGGCGATGCCGCCAACCCCCAGCCCGTTTGCGGCCCCTGCGTTCCCAGACCC‑GAGGCGCGCCACCAAAAAAAG‑CCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATaa                                                                                                      <  2:696061/148‑1 (MQ=255)                                                 gccgGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATg                                                                                                 >  1:213550/1‑151 (MQ=255)                                                  ccgAAAAGTGCCGTCCCGCCGCCCACGACCGGGGCGATGACGTAAAACTCCAGACCGTTTGCGGCCCCTGCGTTACCAGACCC‑GAGGCGCGCCGCCAAAAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATgc                                                                                                <  1:724752/151‑1 (MQ=255)                                                  ccgAAAAGGGCCGTACCGCCGCCCACGCCCGGGGCGATGACGTCAAACCCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCAAAAAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGa                                                                                                    <  2:107083/147‑1 (MQ=255)                                                    ggAAAGGGCCGACCCGGCGCCCGCGACGGGGGCGATGACGACAACCGCGGGACGGTTTGCGGCCCGTGCGTTCCCAGACGG‑GAGGCGGGCGGCAAAAAAAAT‑GCGGGGCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGaa                                                                                                   <  2:117322/146‑1 (MQ=255)                                                    gaaaaGTGCCGTCCCGCCGACCCCGCCCGCGGCGATGACGTAAACCCCCAGACCGTTTGCGGCCCCGGCGTTCCCAGACCC‑GGGGCGCGCCGCAAAAAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATgcg                                                                                               <  1:948367/148‑1 (MQ=255)                                                      aatgggcctacccgccgCCCAGGGCCGGGGCAAGGACGTAAAACCCCGAGCTTTTTGGGGCACCTGTATTCCCAGAACC‑GAGGCGCGCCGCAAAAAAAAT‑GGCGGCCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGaa                                                                                                   <  2:887733/133‑1 (MQ=255)                                                      aaaGTGCCGTACCGCCGCCCGCTACGGGGGCGATGCCGTAAAACACCAGACCTTTTGCGGCCCCTGCGTTACCAGAACC‑GGGGCGCTCCCCAAACAAATC‑GCCGTCCCCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCa                                                                                             <  1:606867/150‑1 (MQ=255)                                                       aaGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATCATCCCGAAAGGGTAACGATAAGAATGCGCAcc                                                                                           >  2:720526/1‑151 (MQ=255)                                                            ccGTCCCGCCGCCCACGCCCGCGGCGATGACGTCAAACCCCAGCCCGTTTGCGGCCCCTGCGTTACCAGAACC‑GAGGCGCGCCGCAAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCcg                                                                                         <  1:598503/148‑1 (MQ=255)                                                                cccgccgCCCCCGACCGCGGCGATGACGCCAAACTCCAGCCCGTTTGCGCCACCTGGTTTCCCGAAACG‑GAGGCGCGCCGCCAAAAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAAc                                                                                   <  1:40566/149‑1 (MQ=255)                                                                  cgccgACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGtt                                                                                >  2:838963/1‑151 (MQ=255)                                                                              ccGCGGCAATGACGTCAACCTCCAGCCCGTTGGGGCCACCGGCGTTACCAGACCC‑GAGCCGCGCCGCCACAAAAAC‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCg                                                                         <  1:751905/146‑1 (MQ=255)                                                                                  ggcgATGACGTCAAACTCCAGCCCGTTTGCGGCCCCTGCGTTCCCAGACCC‑GAGGCGCGCCGCCAAAAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTgc                                                                <  1:316471/151‑1 (MQ=255)                                                                                        gACGTCAAACTCCAGACCTTTGGCGACCCCTGCGTTACCAAACCC‑GAGCCGCGCCGCAAAAAAAAT‑CCGGTTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTgcgc                                                              <  1:794902/147‑1 (MQ=255)                                                                                                   ccAGACCGTTTGCGGCACCTGCTTTCCCAGAACC‑GAGGCCCCCCCCAAACAAAAT‑GCCGCTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTAcc                                               <  1:597507/151‑1 (MQ=255)                                                                                                           tttgggcccccggggTTACAAGACCG‑GGGGCGCCCCCCAAAAAAAAG‑GCGGGCCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAAc                                         <  1:159654/135‑1 (MQ=255)                                                                                                           tttGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACgg                                       >  2:734292/1‑151 (MQ=255)                                                                                                           ttggCGGCCCCTGCTTTACCAAACCC‑GAGGCGCGCCCACAAAAAAAG‑GCGGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCg                                              <  2:739436/141‑1 (MQ=255)                                                                                                            ttGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACg                                        >  2:905496/1‑149 (MQ=255)                                                                                                            tggCGGCACTTGC‑TTTCCAAAACCGGGGGCGCGCCGCAAAAAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACgg                                       <  1:139123/148‑1 (MQ=255)                                                                                                                  ccccggCGTTCCAAGACCC‑GGGGCGCGCCGCAAAAAAAAG‑GCCGTTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCaaaa                                  <  1:534398/144‑1 (MQ=255)                                                                                                                  cACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAAc                                >  2:292304/1‑151 (MQ=255)                                                                                                                   aCCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAAcc                               >  1:316890/1‑151 (MQ=255)                                                                                                                       gCGTTCCCAGACCC‑GAGGCGCGCCGCAAAAAAAAT‑GCCGTTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCCCCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCaaaa                                  <  2:171387/144‑1 (MQ=255)                                                                                                                            aCCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCg                      >  2:221705/1‑151 (MQ=255)                                                                                                                               aGAACC‑GAGGAGTGCCGCCAACAAAAC‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGACAACGCCAAAAACCGAGCGccc                       >  2:606568/1‑147 (MQ=255)                                                                                                                                    cgggggCGCCCCCCAAAAAAAAT‑CCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCg                <  1:661632/146‑1 (MQ=255)                                                                                                                                    c‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGt              >  1:906174/1‑151 (MQ=255)                                                                                                                                        gccgcgcCGCCACAAAACG‑GCCGGCCCCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACACCTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAgg                  <  1:646684/142‑1 (MQ=255)                                                                                                                                              cgcccAAAAAAAG‑GCCCGCCCCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCt     <  2:438345/148‑1 (MQ=255)                                                                                                                                                 ccAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCtgat  >  1:641328/1‑151 (MQ=255)                                                                                                                                                 ccAAAAAAATGGCGGGCCCCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACGGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGtt             <  2:314323/141‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    CGTAATCACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACC‑GAGGCGCGCCGCCAACAAAAT‑GCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGAT  >  NC_000913/2675959‑2676252

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑