Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	71.9%	10.6 / 19.0	32	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (1/8);  new base T (23/0);  total (24/8)
Fisher's exact test for biased strand distribution p-value = 8.56e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.29e-02

GTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGG  >  NC_000913/3206289‑3206565                                                                                                                                                   |                                                                                                                                   gtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCATATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGa                                                                                                                                <  2:482649/151‑1 (MQ=255)        gCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGTAATTTTTCAGAaaaa                                                                                                                            >  1:62178/1‑148 (MQ=255)        gCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAaaaaaa                                                                                                                            >  1:539011/1‑148 (MQ=255)               aTTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATAaaaaaa                                                                                                                    >  2:190455/1‑149 (MQ=255)                  gCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTgg                                                                                                                <  2:465376/150‑1 (MQ=255)                             ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGAATTTTTTCAAAAAAATAAAAAAAATGGAGTTggc                                                                                                         >  1:82732/1‑144 (MQ=255)                               ctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGAGAAATTTTTCACAACAAAATAAAAACAGGAg                                                                                                              >  1:322569/1‑139 (MQ=255)                                  gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCCCATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCatg                                                                                                      <  1:570301/144‑1 (MQ=255)                                   cgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAACAAAAACTTGAGGTGCCATGATTAGCg                                                                                               >  2:135662/1‑150 (MQ=255)                                          ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAAAAAAAACAAAAAATGGAGTTGGCATGATGAGGggaaggaa                                                                                        >  1:474330/1‑150 (MQ=255)                                             attcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACAAAAACTGGAGTTGGCATGGTGAGCggaaggaa                                                                                        >  2:180980/1‑147 (MQ=255)                                                 ttATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCCGACAAATAAAAAAAATTGAGTTGCCATGATGAGGGAAAATAATAAACaa                                                                                 >  2:639461/1‑150 (MQ=255)                                                   aTTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGAAAAAAACAAAAAATGGAGTTGCCATGATGAGCGAAAGTAATAAACaa                                                                                 >  1:459095/1‑148 (MQ=255)                                                     tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACAAAAAATGGAGGTGGCATGATGAGGGAAAATAATAAACAAAAgg                                                                             >  2:457858/1‑150 (MQ=255)                                                     tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                             <  2:441964/150‑1 (MQ=255)                                                       tCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAAACAAATAAAAAAAATGGAGGTGCCATGATGAGGGAAAAAAAAAAacaaca                                                                               >  1:520946/1‑146 (MQ=255)                                                           gTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAAAACAAAAAAAGGAGGTGTCCTGATGAAGGAAAGTAAAAAGCAACAGGccggg                                                                        >  2:601019/1‑145 (MQ=255)                                                                ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCCAACAAAAACAAAAAATGGAGGTGCCATGATGAGGGGAAGGAATAAGAAAAAAGCAGGGAATa                                                                    >  2:626021/1‑148 (MQ=255)                                                                   aCGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAAAAAAAAAAATGGAGGTGCCATGATGAGCGAAAGAAAAAAACAACAAGCAGGGAATAAgat                                                                >  2:477634/1‑147 (MQ=255)                                                                      aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCCGACAAATACAAAAAACGGGGGTGCCCTGATGAGCGGAAGTAATAAACAACAAGCAGGGAAAAAATTGAc                                                             >  2:65621/1‑149 (MQ=255)                                                                        cTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATAAAAAAAATGGAGTTGCCATGATGAGCGAAAATAATAAAAAACAAGCAGTGAATAAGTTGACa                                                            >  2:343773/1‑148 (MQ=255)                                                                         tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGAAATTTTTCAAACAAATAAAAAAAATAGAGTTTGCATGATGGGCGAAAGTAAAAAAAAAAAAGCAATGAATaaagtgata                                                            >  1:58119/1‑140 (MQ=255)                                                                              aTTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGTGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTc                                                   <  1:543832/151‑1 (MQ=255)                                                                              aTTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAAAAAAAAAAAAAAAATGGAGTTGTCCTGATGAGGGAAAGTAATAAACAACAAGCAGGGAATAAATTGAACGAGATTGtt                                                   >  1:225469/1‑150 (MQ=255)                                                                                                cAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGAAAAATACAAAAAATGGGGTTGGCATGGTGAGCGAAAAGAATAAGAAAAAAGAAGTGAATAAATTGACAGAAAATGTCGCTAAACTTAACGcc                                    >  1:614548/1‑148 (MQ=255)                                                                                                 aaaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGGGGTGCCCAGATGAGCGAAAGTAATAAACAACAAGCAGAGAATAAAATGACAGAGAATGTCGCTAACTTTACcccc                                    >  2:331614/1‑147 (MQ=255)                                                                                                     aaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGATTTTTTCAAAAAAAAAAAAAAACTGGAGTTGGCCTGGTGAGGGAAAGAAATAAACAAAAAGCAGTGGATAAATTGACAGAGATTGTCGCTAACTTTAACGCCATGGtt                              >  1:562040/1‑149 (MQ=255)                                                                                                           aaaCCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCg                      <  2:521205/151‑1 (MQ=255)                                                                                                                acaTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCACAAAAAAATAAAAAATGGAGTTGCCATGATGGGGGAAAGTAATAAAGAAAAGGCAGGGAATAAATTGAAAGAGAATGTCGCTAAATTTACCGCCATGATTTCTAACCCaa                    >  1:704079/1‑148 (MQ=255)                                                                                                                 caTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGAAAAATAAAAAAAATGGAGGTGCCCTGATGAGGGGAAGGAATAAACAAAAAGCAGTGAAAAAATTGACAGAGAATGTTGCTAAATTTTCCCCCATTATTTTTAACCCAAAGcc                >  2:238074/1‑151 (MQ=255)                                                                                                                    ttttAGTGGTAGTTTGTGGCGGTAAATTTTTCCAGAAAAATAAAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtg              <  1:190412/150‑1 (MQ=255)                                                                                                                                tttGGGGCGGTGAATTTTCCCAGACAAATACAAAAACTGAAGTTGCCATGATGAGCGAAATTAATAAGCAACAGGCAGTGAATATGTTGACAGATATTGGCGTTAACTTGACCGCCATGATTTCTACCCGAATGCCTGATGACGtggtgg  <  2:498911/150‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                   GTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGG  >  NC_000913/3206289‑3206565

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑