Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,536,190	0	T	G	44.0%	80.1 / 12.6	50	intergenic (+159/+424)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
Reads supporting (aligned to +/- strand):  ref base T (6/22);  new base G (22/0);  total (28/22)
Fisher's exact test for biased strand distribution p-value = 5.24e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCT  >  NC_000913/4536040‑4536339                                                                                                                                                       |                                                                                                                                                       aGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGt                                                                                                                                                        <  1:507973/151‑1 (MQ=255)  gCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTg                                                                                                                                                       <  1:151072/151‑1 (MQ=255)  gCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTg                                                                                                                                                       <  2:502753/151‑1 (MQ=255)         aTGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑Gtttt                                                                                                                                                 >  2:516126/1‑149 (MQ=255)           gATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑Gtttt                                                                                                                                                 >  2:518419/1‑147 (MQ=255)              acgggAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATg                                                                                                                                          <  2:3776/148‑1 (MQ=255)               cAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATga                                                                                                                                         <  2:787745/151‑1 (MQ=255)               cAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATga                                                                                                                                         <  1:475269/151‑1 (MQ=255)                      agtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGaaaa                                                                                                                                  <  2:614658/151‑1 (MQ=255)                        taAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTATGAATGAAAGaaaa                                                                                                                                  >  2:310032/1‑149 (MQ=255)                               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                                                                             <  2:363400/151‑1 (MQ=255)                                                                           cGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCatat                                                                             <  1:302784/151‑1 (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                                                 <  2:242140/150‑1 (MQ=255)                                                                                                        tACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTc                                                 <  2:914751/150‑1 (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)                                                                                                                                                       |                                                                                                                                                       AGCCGTTCATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCT  >  NC_000913/4536040‑4536339

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑