Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	46.0%	42.7 / 33.1	50	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (3/24);  new base T (23/0);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 2.43e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACA  >  NC_000913/3206289‑3206578                                                                                                                                                     |                                                                                                                                                 gtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCa                                                                                                                                                >  2:422063/1‑149 (MQ=255) gtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAg                                                                                                                                               <  1:96556/150‑1 (MQ=255)     ttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACaa                                                                                                                                           >  1:123594/1‑150 (MQ=255)      tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACaaa                                                                                                                                          <  2:146265/150‑1 (MQ=255)       cGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAAt                                                                                                                                         <  2:408376/150‑1 (MQ=255)            aaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAACTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑GATTTTTTCCGCCAAATACaaa                                                                                                                                    >  1:161317/1‑150 (MQ=255)              cATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAAc                                                                                                                                 <  1:358400/151‑1 (MQ=255)                    cATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGG‑AATTTTTCC‑GAcaaaaacaaaaaaatgag                                                                                                                            >  1:332398/1‑144 (MQ=255)                      ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAATACAAAAAATGGAGtt                                                                                                                          >  1:5624/1‑150 (MQ=255)                          cTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAATAAAAAAAATGGAGGTGCCat                                                                                                                     >  1:691593/1‑151 (MQ=255)                            gCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCat                                                                                                                     <  1:399550/149‑1 (MQ=255)                            gCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCat                                                                                                                     <  2:382123/149‑1 (MQ=255)                               ctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AAATTTTTCAGAAAAAAATAAAAAATAGGGGTGCCaggatg                                                                                                                 >  2:218248/1‑150 (MQ=255)                                       atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAAACAAAAAAAAAAAAAGGAGTTGGCATGGTGTGC‑Ggaa                                                                                                         >  2:284505/1‑149 (MQ=255)                                                   aTTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAg                                                                                           <  2:550027/151‑1 (MQ=255)                                                     tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGC‑G‑AAATTTTTTAAACAAAAAAAAAAAATGGAGTTGGCATAGTGAGC‑GGAAGaaataaaaaaaaag                                                                                          >  2:29194/1‑142 (MQ=255)                                                      ttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTTAGACAAAAAAAAAAAAAGGGGTTGGCCTGAGGAGC‑Ggaaagaaaaaaaaaaa                                                                                            >  2:439329/1‑134 (MQ=255)                                                            ttGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTTAAAAAAATACAAAAAATGGGGTTGGCATGATGAGG‑GAAAATAATAAACAAAAGGCAGAGaa                                                                                   >  2:264726/1‑150 (MQ=255)                                                               aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAg                                                                               <  2:573397/151‑1 (MQ=255)                                                                 tCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGt                                                                              <  1:357051/150‑1 (MQ=255)                                                                  cACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAAAAAAAAATTGAGTTGGCATGATGAGG‑GGAAATAATAAAAAACAAGGCGTGAaaaa                                                                                >  1:441884/1‑147 (MQ=255)                                                                  cACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTg                                                                            <  2:56636/151‑1 (MQ=255)                                                                  cACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTg                                                                            <  2:567782/151‑1 (MQ=255)                                                                     gAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAAATTTTTCCA‑AAAAAAAAAAAAAATGGAGTTGGCATGGTGAGG‑GGAAGGAAAAAACAACAAGCAGAGAATaaagt                                                                             >  2:41414/1‑144 (MQ=255)                                                                      aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AAATTTTTCAAACAAAAAAAAAAAAATGAGTTGGCATGATGAGA‑GAAAGTAATAAAAAAAAAGCAGAGAAAAAGATGaa                                                                          >  2:34370/1‑148 (MQ=255)                                                                       aCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGTTAGTTAGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTAGCCACGATGAGC‑TTAAGGAATAAGCACCAGGCAGTGAATAAGTTAACag                                                                        <  2:502424/150‑1 (MQ=255)                                                                       aCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACaga                                                                       <  1:504985/151‑1 (MQ=255)                                                                              aTTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTc                                                                <  2:534368/151‑1 (MQ=255)                                                                                 aCATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCt                                                             <  1:227709/151‑1 (MQ=255)                                                                                  cATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCCGACAAAAAAAAAAAATGGAGTTGCCATGATGAGC‑GAAAGGAAAAAGCAACAGGCAGTGAATAAGTTGACAGAGAATGTCg                                                               >  1:369165/1‑148 (MQ=255)                                                                                  cATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAACAAAAAATTGAGTTGCCATGATGAGC‑GAAAGGAATAAACAACAAGCAGGGAATAAGTTGACAGAGAATGt                                                                 >  1:450964/1‑146 (MQ=255)                                                                                        cACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAAAAAAAAAAGGAGGTGCCATGATGAGC‑GGAAAAAAAAAACAAAAAGCAGGGAAAAAAATGAAAGAGATTGTCGCTAACttt                                                       >  1:639217/1‑150 (MQ=255)                                                                                        cACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTa                                                      <  1:367200/151‑1 (MQ=255)                                                                                        cACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTa                                                      <  1:2811/151‑1 (MQ=255)                                                                                          cGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAACAAAAACTGGAGGTGTCCTGATGAGG‑GAAAGTAATAAACAACAAGCAGTGGATAAGTTGACAGAGATTGTCGCTAACTTTAcc                                                    >  1:729984/1‑151 (MQ=255)                                                                                                 aaaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGAAAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATg                                              <  2:381140/150‑1 (MQ=255)                                                                                                  aaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAATACAAAAAATGGGGTTGCCATGATGAGC‑GAAAGGAATAAACAACAGGCAGGGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCCTg                                              >  1:684899/1‑149 (MQ=255)                                                                                                     aaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAAAAAAAAATGGAGGTTGCATGGTGGGG‑GGAAGGAATAAACAAAAAGCAGAGAAAAAAGTGAAAGAGAATTTCGCTAACTTTTACCCCCTGAttt                                          >  2:463317/1‑150 (MQ=255)                                                                                                        ataAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAAACAAAAACAAAAACTGGAGTTTGCATGGTGGGC‑GGAAGTAATAAACAACAAGCAGAGAAAAAATTGACAGAGATTGTCTCTAAATTTACCGCCATGAttttt                                        >  2:73340/1‑147 (MQ=255)                                                                                                          aaaaCCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTAccc                                    <  1:511822/151‑1 (MQ=255)                                                                                                            aaCCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑ACTTTTTTCCAACCAAAATAAAAAAAGGAGTTTTCCTGATGAGC‑GAAAGTAATAAACAACAAGCAGTGAATAATATTACAGAGATTTTCGCTAACTTTACCGCCATAATTTCTTcc                                     >  2:489823/1‑148 (MQ=255)                                                                                                             aCCACATTTTTAGTGGTAGTTTGTGGCGGG‑G‑AATTTTTTCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GGAAGGAATAAGCAACAGGCAGTGAATAAATTGACAGAGATTGTCGCTAAATTTACCCCCATGATTTCTAccc                                    >  1:277760/1‑148 (MQ=255)                                                                                                                acaTTTTTAGTGGTAGTTTGTGGCGGT‑G‑GATTTTTTCCGTCCAAAAAAAAAAATGGAGTTGGCAATATGGGCGGGAAGGAA‑AAAAAAAAGGCAAGGAATTAATAGAGAGAGATTGGTGCTAACTTTAACGCCAAGATTTTTAccccca                                 >  2:676165/1‑145 (MQ=255)                                                                                                                        aGTGGTAGTTTGTGGCGGT‑G‑GAATTTTTCAAACAAACACAAAAAATGGAGTTTTTCTTATGGGG‑GAAAGTAATAAGCAAAAAGAAGGGAAAAAGTTGTGAGAGATTGTTGCCAACTTTTACGCCACGATTTTTACCCGAAAGcc                             >  2:617929/1‑144 (MQ=255)                                                                                                                                 ttGTGGCGGT‑A‑ATTTTTTCAAGACAAATAAAAAACCTGGATTTGCCATGATGAGC‑GAAAGTAAGAAGCAACAGGCAGTGAATAATTTGAGAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa              <  1:136189/150‑1 (MQ=255)                                                                                                                                     ggCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATaaa          <  1:735021/150‑1 (MQ=255)                                                                                                                                     ggCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAAc         >  2:48831/1‑151 (MQ=255)                                                                                                                                              aaTTTTTCCAGAAAAAAAAAAAAACGGGAGTTGCCATGATGAGC‑AAAAGTAATAAGCAACAGGGAGTAAATAAGTTGACAGAGATTGTCGTTAATTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACa  <  1:730322/151‑1 (MQ=255)                                                                                                                                              aaTTTTTCAAAACAAATACAAAACCGGGATTTGCCTGGATGAGC‑GAAAGTAAGAAGCAACAGGCAGTTAATAATTTAACAGAGTTTGTCGTAAATTTTACCGCCATGATTTCGACCCGAATGCCTGATGACGTGGTGGATAAACTAAAAc   <  2:303728/150‑1 (MQ=255)                                                                                                                                              aaTTTTACCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaaaa    <  2:85722/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                 GTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGC‑GAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACA  >  NC_000913/3206289‑3206578

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑