Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,536,197	0	A	T	42.3%	68.3 / 37.1	52	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
Reads supporting (aligned to +/- strand):  ref base A (3/27);  new base T (22/0);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 8.50e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGC  >  NC_000913/4536047‑4536344                                                                                                                                                       |                                                                                                                                                     cATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTa                                                                                                                                                      <  2:498354/151‑1 (MQ=255)  aTGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAg                                                                                                                                                     <  1:54197/151‑1 (MQ=255)       aCAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAAt                                                                                                                                                 <  1:797599/150‑1 (MQ=255)        cAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATga                                                                                                                                               <  1:77114/151‑1 (MQ=255)          ggAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATgaaa                                                                                                                                             <  2:828566/151‑1 (MQ=255)                   aaGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgca                                                                                                                                    <  2:705155/151‑1 (MQ=255)                     gggCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGGATGAAAGaaaaaaca                                                                                                                                    >  2:530180/1‑145 (MQ=255)                         atatTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCaat                                                                                                                              <  1:300084/151‑1 (MQ=255)                             tttACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCaataat                                                                                                                           <  2:629789/150‑1 (MQ=255)                              ttACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAataata                                                                                                                          <  1:410807/150‑1 (MQ=255)                               tACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAataatat                                                                                                                         <  2:481833/150‑1 (MQ=255)                                   aaTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAt‑aataa                                                                                                                   <  2:906169/151‑1 (MQ=255)                                        tAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTGGAATGAAAAAAAAAGCAAAGAAAAAAAA‑AATAATAGcc                                                                                                              >  1:87759/1‑151 (MQ=255)                                         aaGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTTGGATGAAAAAAAAAGCAAGCAATAATAt‑aaaaa                                                                                                                   >  2:593329/1‑145 (MQ=255)                                           ggCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGCATAAAAAAAAAAGCAAGAaataaaaaaaaaaaag                                                                                                                 >  2:622161/1‑135 (MQ=255)                                               aCTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGTTTTTGGAATGAAAAAAAAAGCAAGCAATAAAAT‑AAAAATAGCCTAAttt                                                                                                        >  2:446893/1‑150 (MQ=255)                                                    ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTg                                                                                                   <  2:723676/150‑1 (MQ=255)                                                             tGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCAtt                                                                                          <  2:153944/150‑1 (MQ=255)                                                                   tCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCat                                                                                    <  1:93506/150‑1 (MQ=255)                                                                       cTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTGTTATGAAAAAAAAAGCAAGCAATAATAT‑AATAAAAGGCTAATTTTTTTTAAAATCATTAAACATatca                                                                                >  1:378711/1‑150 (MQ=255)                                                                         ttCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGTTATGAAAAAAAAAGCAAGCAAAAAAAT‑AATAAATGGCTAAATTTTTTGAAAAACAtttaaaata                                                                                   >  1:850129/1‑138 (MQ=255)                                                                         ttCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATatcatc                                                                              <  2:175777/150‑1 (MQ=255)                                                                         ttCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATatcat                                                                               <  2:621712/149‑1 (MQ=255)                                                                         ttCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATatcat                                                                               <  1:128049/149‑1 (MQ=255)                                                                              gATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGt                                                                         <  1:82563/150‑1 (MQ=255)                                                                              gATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGt                                                                         <  2:212782/150‑1 (MQ=255)                                                                               aTTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGAATGAAAAAAAAAGAAAGGAAAAAAAA‑AATAAAAGCCTTATTTTTTTTAAAAACATTAAAAATattataatct                                                                          >  2:749707/1‑147 (MQ=255)                                                                                ttATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGGTTTTGGTATAAAAAAAAAAACAAGCAATAATAT‑AAAAAAAAACTTAGTTTTTTTAACATCAATAAACATatcatcataggct                                                                       >  1:104330/1‑145 (MQ=255)                                                                                               tttACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTTGAATTAAAAAAAAAGCAAGAAAAAATAT‑AATAATGGGCTAATTTTTTTTTAAATCATTAAGCATATCATCATCGTTTATTTTTCAGAATccct                                                       >  1:581433/1‑149 (MQ=255)                                                                                                 tACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGTATGAAAAAAAAAACAAGCAAAAAAAT‑AATAAAAGCCTAATTTTTTTTAACATCATTAAACATATCATCATCGTCTATTTTTCCGAATCCGTCg                                                     >  1:522271/1‑151 (MQ=255)                                                                                                     tAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGAATGAAAAAAAAAGCAAGCAAAAATAT‑AATAAAAGGCTAATTTTTTTTTACAACATTAAGCATATAATCCTCTTCTTTTTTTCAGAATACGTCGACtt                                                 >  2:175518/1‑151 (MQ=255)                                                                                                       aTCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCGTTTTGGAATGAAAGAAAAAGCAAGGAAAAAAAT‑AATAATAGTCTAAATTTTTTGGACATCATTAAGGAAATCATTATTGTCTATTTTCCAGAATCCGTCgcact                                                 >  2:438622/1‑145 (MQ=255)                                                                                                          aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGTATGAAAAAAAAAACAAGGAAAAAAAT‑AATAAAGGGCTAATTTTTTTGAAAATCATTAAGCATATAATCATCGTCTATTTTTCAGAATTCCTCGACtt                                                 >  1:253345/1‑146 (MQ=255)                                                                                                           ttttCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGAATGAAAAAAAAAACAAACAAAAAAATAAAAAATGGCCAATTTTTTTTGAA‑ATCATTAAACAAATCATTATCGGTTATTTTTCAAAATCCGGCGAATTTTaa                                             >  1:918858/1‑149 (MQ=255)                                                                                                            tttCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGTTTTTTGAAAGCAAAAAAAAGAAACAAAAAATAT‑AATAAAGGGCTAATTTTTTTTTGCAATAATAAATAAATCATCATTTTCTCTTTTTTCGAATCCGCCGAATTATTATcc                                          >  2:642573/1‑150 (MQ=255)                                                                                                            tttCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCCTTTTTGAATGAAAAAAAAAGCCAGCAAAAATAT‑AATAATAGCCTAATTTTTTTTTACATCATTAAACATATCATCATCCTCTATTTTCCAGAATCCGTCGACCTATaa                                             >  1:372294/1‑148 (MQ=255)                                                                                                               ccTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCa                                       <  2:94156/151‑1 (MQ=255)                                                                                                               ccTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCa                                       <  1:39650/151‑1 (MQ=255)                                                                                                                cTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGGATGAAAGAAAAAGCAAGCAATAATAT‑AATAAAGGCCTAATTTTTTTTAACATCATTAAACATATCATCATCGTCTATTTTCCAGAAACCGTCGACTTATAATCGcc                                        >  2:838453/1‑149 (MQ=255)                                                                                                                  ttGCATAATGCGCCTGGGATTAATGGCGGGGGCGTTTTGGAATGAAAAAAAAAGCAAGCAAAAATAT‑AAAAATGGGCTAATTTCTTTTAAAAAAATTAAAAATAACATCATAGTCTATTTTTCAGAATCCGTCGACTTATaaaaacca                                       >  1:682996/1‑142 (MQ=255)                                                                                                                    gCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACg                                  <  2:749736/151‑1 (MQ=255)                                                                                                                      aTAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGAATGAAAGAAAATGCAAGCAAAAATAT‑AATAAAAGCCTTATTTTTTTTAACATCATTAAACATATCATCATCGTCTATTTTCCAGAAACCGTCGACTTATAATCGCCCGAACgg                                 >  2:829679/1‑150 (MQ=255)                                                                                                                      aTAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGc                                <  1:192230/151‑1 (MQ=255)                                                                                                                       tAATGCGCCTGGGATTAATGGCGGGGGGTTTTTGGGATGAAAAAAAAAAGAAGCAAAAAAAT‑AATAAAGGCCTTATTTTTTTTAAAATCATTTAACATATCATCATCGTCTATTTTTCAGAATCCGTCGACCTATAATCGCCAGaa                                    >  1:586336/1‑146 (MQ=255)                                                                                                                       tAATGCGCCTGGGATTAATGGCGGGGGGCTTTTGGGATAAAAAAAAAAGCAACCAAAAAAAT‑AAACAAAGACTAATTTTTTTGATCATCACTAAACATATCAACATCGTTTTTTTTGCCGAATCCCTCGACCTTTTATATCCAGAAAgg                                 >  1:183148/1‑149 (MQ=255)                                                                                                                        aaTGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCat                              <  2:222851/151‑1 (MQ=255)                                                                                                                           gcgcCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATc                           <  1:593264/151‑1 (MQ=255)                                                                                                                           gcgcCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATc                           <  2:329353/151‑1 (MQ=255)                                                                                                                              ccTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAgg                        <  1:902331/151‑1 (MQ=255)                                                                                                                                          ggCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCg             >  1:27428/1‑150 (MQ=255)                                                                                                                                                 gCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCtgt     <  2:479691/151‑1 (MQ=255)                                                                                                                                                    tttAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGc  >  1:312169/1‑151 (MQ=255)                                                                                                                                                    tttAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGc  >  2:356840/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                     CATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGC  >  NC_000913/4536047‑4536344

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑