Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	43.8%	49.0 / 25.6	48	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (1/26);  new base T (21/0);  total (22/26)
Fisher's exact test for biased strand distribution p-value = 9.86e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTA  >  NC_000913/3206286‑3206582                                                                                                                                                       |                                                                                                                                                    aGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTcc                                                                                                                                                    <  1:308541/151‑1 (MQ=255)          cGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGTGATTTTTTcccacaaa                                                                                                                                              >  1:776220/1‑143 (MQ=255)             aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACaa                                                                                                                                        <  1:600139/151‑1 (MQ=255)                     gCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTgg                                                                                                                                 <  2:982503/150‑1 (MQ=255)                     gCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTgg                                                                                                                                 <  1:839174/150‑1 (MQ=255)                        aTTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCCAACAAAAAAAAAAAATGGAggt                                                                                                                             >  2:750979/1‑149 (MQ=255)                        aTTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGtt                                                                                                                             <  2:906163/151‑1 (MQ=255)                         ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACAAAAACAAAAAATGGAGtt                                                                                                                             >  2:590099/1‑150 (MQ=255)                         ttCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                               <  2:420695/148‑1 (MQ=255)                            ccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGGATTTTTTCCGACAAATACAAAAACTGGAGTTgtc                                                                                                                          >  1:714409/1‑148 (MQ=255)                                       gcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGGATTTTTTCAGACAAATACAAAAAAATGGGTTGCCatggagtggg                                                                                                                >  2:304380/1‑142 (MQ=255)                                       gcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGaa                                                                                                              <  1:260501/151‑1 (MQ=255)                                        cAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGaaa                                                                                                             <  2:230148/151‑1 (MQ=255)                                          atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACAAAAAAAAAAAATGGAGTTTTCCTGATGAggggaa                                                                                                             >  1:453178/1‑144 (MQ=255)                                            attcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGtaa                                                                                                         <  1:714297/151‑1 (MQ=255)                                                attcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAg                                                                                                     <  1:38284/151‑1 (MQ=255)                                                      aTTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACAAAAAAAAAAACTGGAGGTGCCATGATGGGCGAAAGTAAAAAACaa                                                                                                  >  2:627019/1‑148 (MQ=255)                                                              gTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                                       <  2:511310/151‑1 (MQ=255)                                                                 gATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATaa                                                                                    <  1:981696/151‑1 (MQ=255)                                                                  aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAg                                                                                   <  1:64140/151‑1 (MQ=255)                                                                    tCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAAACAAAAACAAAAAAAGGAGTTTGCATGATGAGGGAAAGTAATAAACAACAGGCAGAGAATa                                                                                     >  1:195379/1‑147 (MQ=255)                                                                     cACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGtt                                                                                 <  2:935270/150‑1 (MQ=255)                                                                        gAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGGATTTTTTCAGACAAAAAAAAAAAATGGAGGTGCCATGATGAGGGGAAGAAATAAGCAAAAAGCAGGGAATaaagt                                                                                 >  2:729192/1‑144 (MQ=255)                                                                                    aCATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCt                                                                 <  2:791174/151‑1 (MQ=255)                                                                                     cgtatTCACGGTGGCAAAAAATATAAAACCACAGTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTa                                                                <  2:668223/149‑1 (MQ=255)                                                                                     cATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACAAATACAAAAAATGGAGGTGCCCTGATGAGCGGAAGTAATAAACAAAAAGCAGGGAAAAAGTTGACAGAGATTGt                                                                     >  2:74762/1‑146 (MQ=255)                                                                                         ttCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACAAATACAAAAAATGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGGGAATAAATTGACAGAGATTGTCGCTAACtt                                                            >  2:338587/1‑151 (MQ=255)                                                                                             cGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACAAAAAAAAAAAATGGGGGTGCCATGATGAGGGAAAGAAATAAGAAAAAAGCAGGGAATAAGTTGACAGAGATTGTTGCTCAAttt                                                           >  2:787169/1‑148 (MQ=255)                                                                                             cGGTGCCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACAAAAACAAAAACTGGAGTTGCCATGATTAGGGGAAAGAATAAAAAAAAGGGAGGGAAAAAGTTTACAGAGAATGTCGCTAACttt                                                           >  1:898846/1‑148 (MQ=255)                                                                                                  gCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAAATTTTTCAGACAAATACAAAAAATGGAGTTGGCATGATGAGCGGAAGTAATAAACAACAAGCAGGGAAAAAGTTGACAGAGATTGTCGCTAACTTTACCGc                                                      >  2:529490/1‑148 (MQ=255)                                                                                                    aaaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCAt                                                   <  1:547960/149‑1 (MQ=255)                                                                                                     aaaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCCGACAAAAAAAAAAAACGGGGTTTCCATGATGAGGGGAAGTAATAAACAAAAGGCAGTGAATAAGGTGGCAGAGAATGTTGCCAACTTTACCGcc                                                     >  2:201123/1‑146 (MQ=255)                                                                                                       aaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGAttt                                              <  2:369426/151‑1 (MQ=255)                                                                                                        aaTAAAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGAAAAATAAAAAAACTGGAGTTGCCATGATGAGCGAAAGAAATAAGCAACAGGCAGTGAATAAGTGGACAGAGATTGTCCCTACCTTTACCGCCATGATTTc                                             <  1:818896/151‑1 (MQ=255)                                                                                                         atatAAACCCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAACCAACAGGCAGTAAATAAGTTGACAGAGTTTGTCGCTAACTTTACCGCCATGATTTCt                                            <  1:232738/151‑1 (MQ=255)                                                                                                         atatAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACAAAAACAAAAAATGGGGTTGCCATGATGAGCGAAAGGAATAAACAAAAGGGAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGAttttt                                            >  2:66667/1‑149 (MQ=255)                                                                                                           ataAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAAAAAAAAAAAAAAACAGGAGGTGCCATGATGAGGGAAAGTAATAAACAAAAAGCCGGGAAAAAATTGACAGAGATTTTTGCTAAATTTACCCCCCTGAttttt                                            >  1:621038/1‑147 (MQ=255)                                                                                                             aaacCCACATTTTTAGTGGTAGTTTGGGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGAAATAACCAACAGGCAGTGAATAAGTTGACAGAGATTGCCGCTAACTTTACCGCCATGATTTCTAccc                                        <  1:447381/151‑1 (MQ=255)                                                                                                             aaaaCCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTAcc                                         <  2:261693/150‑1 (MQ=255)                                                                                                              aaaCCACATTTTTAGTGGTAGTTTGTGGC‑GGTGGAATTTTTCAAACAAAAAAAAAAAATGGAGGTGGCATGATGAGGGGAAAGAATAAGAAAAAGGCAGAGAATAAAGTGAAAGAGAATGTTGCTAAATTTACCGCCATGATTTTTAccc                                        >  1:283312/1‑150 (MQ=255)                                                                                                              aaaCCACATTTTTAGTGGTAGTTTGTGGC‑GGTAAATTTTTCCAGAAAAATACAAAAACGGGAGTTGCCAGGATGAGCGAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTTTCGCTAACTTTACCGCCATGATTTCTACCCg                                       <  2:975517/151‑1 (MQ=255)                                                                                                                       ttttAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAAACAAATACAAAAAATGGGGGTGGCCTGATGAGGGGAAAGAATAAGCAAAAAGCAGGGAATAAATTGACAGAGATTGTCGCTAACTTTTCCGCCATGATTTTTACCCCAAAGCCt                                >  2:616844/1‑149 (MQ=255)                                                                                                                        tttAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCCGACAAAAACACAAAATTGAGTTGGCATGATTGGGGGAAGTAAAAAAAAAAAGGCAGGGAATAAAGTTAAAGAGATTGTCGCTAACTTTTACGCCATGATTTTTACCCGAAtcactg                               >  1:829011/1‑144 (MQ=255)                                                                                                                        tttAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACAAAAAAAAAAACTGGAGGTGGCATGATGAGGGGAAAGAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTAACGCCCTGATTTTTTCCCGGAAGCCtgat                             >  1:493576/1‑151 (MQ=255)                                                                                                                              ggTATTTTGTGGG‑GGTAAATTTTTCCAGAAAAATACAAAACCTGGAGTTGCCAGGATGAGCAAAAGTAAAAAGCAATAGGCATTGAATAAGTGGACGGAGTTTGTCGCTAATTTTACCGCCATGATTTCTACCCGAATGCCtgatg                            <  1:821971/146‑1 (MQ=255)                                                                                                                               gTAGTTTGTGGC‑GGTGAATTTTTTCAGACAAATAAAAAAAATGGAGTTGCCATGATGAGGGGAAGTAATAAACAAAAAGGAGTGAATAAGATGACAAAGATTGTTGCTAACTTTAACGCCATGATTTTTAACCCAATGCCTGATGACgggg                      >  1:862838/1‑151 (MQ=255)                                                                                                                                        ggC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAAc             <  2:381433/151‑1 (MQ=255)                                                                                                                                            ggTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTa           >  2:478157/1‑150 (MQ=255)                                                                                                                                                aaTTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAAc       <  2:967423/150‑1 (MQ=255)                                                                                                                                                     ttCCAAACAAATACAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAATTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTa  <  1:750836/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                    AGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAAAACAGCTA  >  NC_000913/3206286‑3206582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑