Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,536,212	0	T	A	44.2%	73.0 / 33.8	52	intergenic (+181/+402)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
Reads supporting (aligned to +/- strand):  ref base T (7/22);  new base A (23/0);  total (30/22)
Fisher's exact test for biased strand distribution p-value = 8.45e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCAGTAA  >  NC_000913/4536070‑4536361                                                                                                                                                |                                                                                                                                                      cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GGTTTTTGAGTTAAAAAAAAAgaaagca                                                                                                                                                >  1:131751/1‑150 (MQ=255)  atatTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCaat                                                                                                                                              <  2:392509/151‑1 (MQ=255)    atTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTTGAATGAAAAAAAAAacaaacaaa                                                                                                                                              >  1:242137/1‑148 (MQ=255)     ttttACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTTTGATGAAAAAAAAAGAAAACaataa                                                                                                                                            >  1:202696/1‑150 (MQ=255)      tttACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑GTTTTTTGAATGAAAAAAAAAGAAAACaaaaa                                                                                                                                            >  2:7221/1‑149 (MQ=255)            aaTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTGGAATGAAAGAAAAAACAAACAAaaaaataata                                                                                                                                     >  2:1035966/1‑150 (MQ=255)                  aaGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTGGAATGAAAAAAAAAGAAAACAAAAATAtaaaaaaaggc                                                                                                                               >  2:953860/1‑145 (MQ=255)                  aaGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTTGAATGAAAAAAAAAACAAACAAAAAAAAAATAATAGcc                                                                                                                               >  1:423492/1‑150 (MQ=255)                   aGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTTGAATTAAAAAAAAAGTAAACAAAAAAAtaaaaaaaggct                                                                                                                              >  1:154983/1‑144 (MQ=255)                       gACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTGGGATGAAAAAAAAAGAAAGCAAAAATATAAAAATGGCCTAAttt                                                                                                                         >  2:824770/1‑151 (MQ=255)                          tttCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCCTTTTTTGAAT‑TAAGAAAAAGCAAACAAAAAAAtaaaaaaagaactaattttt                                                                                                                      >  2:436504/1‑137 (MQ=255)                           ttCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCtt                                                                                                                      <  2:186686/150‑1 (MQ=255)                           ttCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCt                                                                                                                       <  1:526295/149‑1 (MQ=255)                             ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGa                                                                                                                   <  2:756965/151‑1 (MQ=255)                             ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGa                                                                                                                   <  1:270450/151‑1 (MQ=255)                              cGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGaa                                                                                                                  <  2:567324/151‑1 (MQ=255)                                   tATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GCTTTTTGAAAGAAAAAAAAAACAAACAAAAATATAAAAAAAGCCTAATttttttttaaa                                                                                                                >  2:616622/1‑143 (MQ=255)                                        cGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTTTAATTAAAAAAAAAAAAAACAATAATATAAAAAAAGGCTCATttttttttaaaaca                                                                                                             >  1:701372/1‑138 (MQ=255)                                           gTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCat                                                                                                     <  2:643511/151‑1 (MQ=255)                                             cGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCatat                                                                                                   <  1:302784/151‑1 (MQ=255)                                             cGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCatat                                                                                                   <  2:363400/151‑1 (MQ=255)                                                   tCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATatcatca                                                                                              <  2:549848/150‑1 (MQ=255)                                                    ccTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATatcatcat                                                                                             <  2:699169/150‑1 (MQ=255)                                                    ccTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTTGGATGAAAAAAAAAGGAAGAAAAAAAATAATAAAAGCCTCATTTTTTTTGACATTATTaaaaat                                                                                                     >  2:19387/1‑138 (MQ=255)                                                                 cTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTTGGGATGAAAGAAAAAGCAAGCAATAATATAAAAAAAGCCTAATTTTTTTTAAAATAATTAAAAATATCATCATCGTCTAtttttc                                                                                 >  2:159952/1‑146 (MQ=255)                                                                   tATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTGGGATTAAAAAAAAAGCAAACAAAAATATAAAAAAAGCCTAATTTTTTTTTAAATCATTAAAAATATTATCATCCTCTATTTTCCAGa                                                                              >  2:395696/1‑150 (MQ=255)                                                                        tttACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTTGAATGAAAAAAAAAGCAAGCAAAAAAATAAAAAAGGGCTAATTTTTTTTAAAAAAATTTAACAAATCATTAACCTCTTATTTTCAGAATcc                                                                          >  2:916568/1‑149 (MQ=255)                                                                          tACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTc                                                                       <  2:914751/150‑1 (MQ=255)                                                                          tACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTc                                                                       <  2:242140/150‑1 (MQ=255)                                                                             cTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑TTTTTTTGGATTTAAAAAAAAACAAGAAAAAAAATAAAAAAAGCCTAATTTTTTTTTAAATAATTAAAAATATAATTATAGTCTATTTTTCAGAAACCGt                                                                        >  1:23003/1‑146 (MQ=255)                                                                                aTCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTTGGATTAAAAAAAAAGCAAGGAAAAAAATAAAAAAAGGCTAATTTTTTTTTAAATCATTAAACATATTATTATAGTTTATTTTTCAGAAACCGTCGACtt                                                                  >  1:7273/1‑149 (MQ=255)                                                                                   aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAAt                                                             <  2:210260/151‑1 (MQ=255)                                                                                     tttCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTTGGATTAAAAAAAAAGCAAGAAAAAATATAATAATAGGCTAATTTTTTTTTAAATCATTAAACAAAATATCATCGTTTTTTTTTCAGAAACCGTCGACTTATaa                                                              >  1:864155/1‑148 (MQ=255)                                                                                              cATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTTGGATGAAAAAAAAAACAAGGAATAAAATAAAAATAGGCCAATTTTTTTTTAAATCATTAAACATATTATCATCGTCTATTTTTCAGAATTCGTCGGCTTATAATAACCAGAAAgg                                                  >  1:245961/1‑151 (MQ=255)                                                                                               aTAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTGGGATGCAAAAAAAAACAAGCAAAAATATAAAAAAGGGCTTATTTTTTTTTACATCATTAAATATATTATTATTGTCTCTTTTTCTAAATCCGTCGACCTTTAATAGcc                                                         >  1:486282/1‑143 (MQ=255)                                                                                                        cTGGGATTAATGGCGGGGG‑CTTTTTTGAATGAAAGAAAAAACAAGCAAAAAAATAATAAAAGGCTAATTTTTTTTTAAAACATTTAACATATCATCATCGTCTATTTTTCAGAAACCCTCGCCTTATaaattcccgaa                                                     >  1:352851/1‑129 (MQ=255)                                                                                                         tGGGATTAATGGCGGGTG‑CTTTTTTGTATGAAAAAAAAAAAAAGCAAAAAAAAAAAAATAGGCTAATTTTTTTTTAAATCATTAAAAATAACATCATCCTCTTTTTTTCAGCATACGTCCTCTTATAATcaacaaca                                                     >  1:819375/1‑130 (MQ=255)                                                                                                               tAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGtgc                                  <  1:293857/150‑1 (MQ=255)                                                                                                                  tGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCg                              >  2:147489/1‑151 (MQ=255)                                                                                                                   ggCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGa                             <  2:98604/151‑1 (MQ=255)                                                                                                                        gTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCt                        >  2:13380/1‑151 (MQ=255)                                                                                                                             ttttAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTgg                    >  1:185428/1‑151 (MQ=255)                                                                                                                                 aGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGccc                 <  1:518410/150‑1 (MQ=255)                                                                                                                                 aGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCa                <  1:310028/151‑1 (MQ=255)                                                                                                                                     aTGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAAc            <  2:250654/151‑1 (MQ=255)                                                                                                                                     aTGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAAc            >  1:127187/1‑151 (MQ=255)                                                                                                                                        aaagaaaATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGtt         >  1:83812/1‑151 (MQ=255)                                                                                                                                           gaaaATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCa      <  2:243342/151‑1 (MQ=255)                                                                                                                                            aaaaTGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCAg     <  2:131752/151‑1 (MQ=255)                                                                                                                                            aaaaTGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCAg     <  1:436496/151‑1 (MQ=255)                                                                                                                                              aaTGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCAGt    >  1:813607/1‑150 (MQ=255)                                                                                                                                               aTGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCAGTa   >  1:1028263/1‑150 (MQ=255)                                                                                                                                                tGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCAGTaa  >  1:891399/1‑150 (MQ=255)                                                                                                                                                |                                                                                                                                                      CATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCAAAACGTTCCAGTAA  >  NC_000913/4536070‑4536361

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑