Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	48.1%	43.7 / 34.0	52	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (6/21);  new base T (25/0);  total (31/21)
Fisher's exact test for biased strand distribution p-value = 1.61e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTA  >  NC_000913/3206289‑3206573                                                                                                                                                     |                                                                                                                                            gtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGa                                                                                                                                         <  1:45452/151‑1 (MQ=255)   aTTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACa                                                                                                                                       <  1:957600/151‑1 (MQ=255)      tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAATATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAACTTTTTCCaaca                                                                                                                                        >  1:168863/1‑145 (MQ=255)       cGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACaaag                                                                                                                                    <  1:747277/150‑2 (MQ=255)       cGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATa                                                                                                                                   <  1:500526/151‑1 (MQ=255)          aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACaa                                                                                                                                <  1:371729/151‑1 (MQ=255)               aTTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCAGACAAATAaaaaaa                                                                                                                             >  2:718562/1‑149 (MQ=255)                    cATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGAGGTAGTTTGTGGCGGAAGAT‑TTTTTCTCAACAAA‑ACaaaaaatcg                                                                                                                         >  1:150477/1‑144 (MQ=255)                      ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCAGAAAAATAAAAAAAATGGAg                                                                                                                       >  2:190630/1‑148 (MQ=255)                      ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑ATTTTTCAGACAAAAAAAAAAAATgg                                                                                                                         >  1:346644/1‑146 (MQ=255)                       tCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCCAAAAAATAAAAAAAATGGAGtt                                                                                                                     >  1:410857/1‑149 (MQ=255)                       tCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTg                                                                                                                    <  2:495514/150‑1 (MQ=255)                          cTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGGA‑TTTTTCCACAACAATAAAAAAACTGGGGGTTCCat                                                                                                                >  2:578472/1‑151 (MQ=255)                           tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑CGGA‑TTTTTTAACAAAAATAAAAAAACTGGGGATGccgt                                                                                                                >  1:209255/1‑148 (MQ=255)                               ctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGGA‑TTTTTTCATAGAAATACAAAAACTCGAGGTGACacgctg                                                                                                            >  2:721297/1‑145 (MQ=255)                                tGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCAGACAAATACAAAAAAAGGAGGTGCCatgatg                                                                                                            >  2:896225/1‑149 (MQ=255)                                 ggCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCAGACAAAAAAAAAAACTGGAGGTGCCatgat                                                                                                             >  2:218334/1‑147 (MQ=255)                                 ggCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGc                                                                                                         <  1:437668/151‑1 (MQ=255)                                             attcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCTCATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAg                                                                                             <  2:528930/151‑1 (MQ=255)                                             attcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAg                                                                                             <  1:6822/151‑1 (MQ=255)                                               tcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGc                                                                                            <  1:482429/150‑1 (MQ=255)                                                    ttttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCAGACAAATAAAAAAAATGGAGGTGCCATGATGAGGGAAAGGAATAAacaaca                                                                                        >  2:880309/1‑149 (MQ=255)                                                     tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGGA‑TTTTTTCAGCCAAAAAAAAAAAATTGAGGTGTCATGATGAGCGGAAATAATAAacaaca                                                                                        >  1:796722/1‑148 (MQ=255)                                                       tCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCCGACAAATACCAAAAACGGAGTTGTCATGATGAGCGGAAAAAATAAGCcaca                                                                                        >  2:892474/1‑146 (MQ=255)                                                             tGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AAt                                                                             <  1:547554/150‑1 (MQ=255)                                                                ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCAGACAAATACAAAAAATGGAGTTGCCATGATGAGGGAAAGTAATAAACAACAGGCAGTG‑AATaa                                                                           >  2:1021405/1‑149 (MQ=255)                                                                   aCGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTg                                                                       <  1:743728/150‑1 (MQ=255)                                                                       aCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑GGAA‑TTTTTTCAAACAAAAAAAAAAAATTGGGTTGCCATGATGAGCGGAAATAATAAAAAAAAAGCAGTG‑GATAAAtt                                                                        >  1:663807/1‑145 (MQ=255)                                                                         tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCAGACAAAAACAAAAAATGGGGATGCCATGATGAGCGAAAGTAATAAACAACAAGCAGTG‑AATAAGTTGa                                                                      >  2:557146/1‑145 (MQ=255)                                                                          gTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACagag                                                                 <  2:723305/149‑1 (MQ=255)                                                                              aTTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCAGACAAATACAAAAACTGGGGGTGCCCTGATGAGCGAAAGTAATAAGCAAAAAGCCGTG‑AATAAGTTGACAGAGATTGt                                                            >  2:764187/1‑150 (MQ=255)                                                                                tACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACAGAGATTGTCg                                                          <  1:580036/150‑1 (MQ=255)                                                                                tACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑ATAG‑ATTTTTTTCACAAAAATAAAAACACGAGTGGCCATAGTGAGTGGAAGAGATAAAAAACAGGCAGCG‑GATAAATTTACAGAGGtttttg                                                          >  1:708404/1‑146 (MQ=255)                                                                                   atatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACAGAGATTGTCGCTaa                                                      <  1:796883/151‑1 (MQ=255)                                                                                   atatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACAGAGATTGTCGCTaa                                                      <  2:244172/151‑1 (MQ=255)                                                                                     atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACAGAGATTGTCGCTAAc                                                     <  1:754366/150‑1 (MQ=255)                                                                                       tCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCAGAAAAAAAAAAAAAATGGAGGTGCCATGATGAGCGAAAGTAAAAAAAAACAAGCAGTG‑AATAAAGTGAAAGAGAATGTCGCTAACttt                                                  >  2:612467/1‑151 (MQ=255)                                                                                             tGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCCGACAAATACAAAAAATGGAGTTGCCATGATGAGCGAAAGAAATAAGCAACAAGCAGGG‑AATAAGTTGACAGCGATTGTTGCTTAATTTACCGcc                                            >  2:221194/1‑151 (MQ=255)                                                                                                 aaaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑AGAA‑ATTTTTCAGACAAATATAAAAAATGGGGTTGGCCTGATTAGGGAAAGAAATAAAGAAAAAGCAGTG‑GATAAATTGTCAAAGATTGTTGCTAAATTTATCGcc                                            >  1:204397/1‑147 (MQ=255)                                                                                                    aaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGGGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCATTG‑AATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGAttt                                     <  1:187831/151‑1 (MQ=255)                                                                                                     aaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTc                                    <  1:196338/151‑1 (MQ=255)                                                                                                     aaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTc                                    <  1:280286/151‑1 (MQ=255)                                                                                                      atatAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑ATTTTTCAGAAAAATAAAAAAAATGGAGTTGGCATGATGAGCGAAAGGAATAAAAAACAAGCAGTG‑AAAAAATTGACAGAGAATGTTGCTAACTTTAACCCCCTGAttt                                     >  1:483797/1‑149 (MQ=255)                                                                                                        ataAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGGA‑TTTTTTCCGACAAATACAAAAAATGGAGTTGGCATGATGAGGGAAAGGAATAAGCAAAAAGCAGGG‑GATAAATTGACAGAGATTGTCGCTTACTTTaaccccccgatt                                      >  2:549931/1‑135 (MQ=255)                                                                                                        ataAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTTCCGACAAAAACAAAAAATGGAGTTGCCATGATGAGCGGAAGGAATAAAAAAAAAGCAGTG‑AAAAAATTGACAGAGAATGTCGCTAACTTTACCGCCCTGAttttt                                   >  2:1010182/1‑147 (MQ=255)                                                                                                           aaaCCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑ATTTTTCAGACAAATAAAAAAAATGGAGTTGCCATGATGAGGGGAAGGAATAAGAAACAGGCAGGG‑GATAAGTTGACAGAGATTGTCGCTAAATTTTCCGCCATGATTTTTa                                  >  1:775914/1‑147 (MQ=255)                                                                                                            aaCCACATTTTTAGTGGTAGTTTGTGGCGG‑AGAATTTTTTCCTCAC‑AATAAAAAAAATGGGGGTGCCAAGAAGGGTCGAAGTAATAAACAAAAAGCAGGGAAAAAAGTTGA‑AAAGATTATCGCTAACATTAACGCCATAATTTCttacc                               >  1:815060/1‑145 (MQ=255)                                                                                                                  aTTTTTAGTGGTAGTTTGTGGCGG‑TGGA‑TTTTTTCAGACCAATACAAAAAATGGAGGTGCCATGATGAGCGAAAGTAATAAGAAAAAAGCAGGG‑AATAAGTTGAAAGAGATTGTCGCTAACTTTACCGCCATGATTTTTACCCCAATGcc                        >  1:1592/1‑150 (MQ=255)                                                                                                                    ttttAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGAAAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtg                      <  1:163738/150‑1 (MQ=255)                                                                                                                           ggTAGTTTGTGGCGG‑TGAA‑TTTTTTCCGACAAATACAAAAAATTGAGGTGCCATGATGAGCGAAAAGAATAAACAAAAGGCAGTG‑AATAAATTGACAGAGATTGTCGCTAAATTTACCGCCATGATTTTTACCCCGATGCCTGATGACggg              >  2:811044/1‑149 (MQ=255)                                                                                                                                       cGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACt   >  2:561484/1‑150 (MQ=255)                                                                                                                                        gg‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTa  >  2:702595/1‑150 (MQ=255)                                                                                                                                                     |                                                                                                                                            GTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGG‑TGAA‑TTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTG‑AATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTA  >  NC_000913/3206289‑3206573

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑