Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,536,197	0	A	T	44.2%	60.7 / 41.4	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 (3/26);  new base T (23/0);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.47e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCC  >  NC_000913/4536053‑4536346                                                                                                                                                 |                                                                                                                                                        aCAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGGTTAATGGCGGGTGCTTTTAGGAAt                                                                                                                                                    <  2:492260/150‑1 (MQ=255) aCAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATg                                                                                                                                                   <  2:3824/151‑1 (MQ=255)    ggAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATga‑aa                                                                                                                                               <  2:476864/151‑1 (MQ=255)     gAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATga‑aag                                                                                                                                              <  2:448635/151‑1 (MQ=255)      agtagtAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATga‑aaga                                                                                                                                             <  1:110087/151‑1 (MQ=255)       gtagtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGTTTTTTGAATga‑aa                                                                                                                                               >  1:288549/1‑148 (MQ=255)          gtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAAt                                                                                                                                         <  2:112509/151‑1 (MQ=255)          gtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTCCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAAt                                                                                                                                         <  1:332476/151‑1 (MQ=255)            aaaGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGAATGA‑AAGaaaa                                                                                                                                          >  1:189589/1‑148 (MQ=255)            aaaGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATgc                                                                                                                                       <  2:22231/151‑1 (MQ=255)            aaaGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGTTTTTGGAATGa‑aaaaaaaa                                                                                                                                         >  1:419929/1‑148 (MQ=255)                  cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATgcaagcaa                                                                                                                                 <  2:307464/151‑1 (MQ=255)                     atTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCaata                                                                                                                               <  2:559629/150‑1 (MQ=255)                       tttACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCATTTGCATAATACGCCTGGGATTAATGGCGGGGGGTTTTTTGTATGA‑AAAAAAATgcaaaacat                                                                                                                                >  2:160509/1‑142 (MQ=255)                          aCCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAataatat‑aa                                                                                                                        <  2:322089/151‑1 (MQ=255)                             aaTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAt‑aataa                                                                                                                     <  1:219342/151‑1 (MQ=255)                                   aaGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGAATGA‑AAGAAAAAAAAAGCAAAAATAT‑AAAAAAGGcc                                                                                                                >  2:222071/1‑150 (MQ=255)                                    aGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTa                                                                                                              <  1:396320/151‑1 (MQ=255)                                           tttCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTGGGATGA‑AAAAAAAAGCAAACAAAAAAATAAAAAAGGGCCAAAttttt                                                                                                        >  1:517635/1‑149 (MQ=255)                                            ttCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCt                                                                                                        <  2:217254/149‑1 (MQ=255)                                            ttCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGCTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGTGCCTTTTTCACTTATAAAAAAAACAAAGAAATCATAT‑TATAATGGTCTTATTTCttt                                                                                                      >  2:636554/1‑151 (MQ=255)                                             tCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCttt                                                                                                      <  1:674407/150‑1 (MQ=255)                                              ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTg                                                                                                     <  2:346258/150‑1 (MQ=255)                                              ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGAATGA‑AAGAAAAAAAAAGCAATAATAT‑AATAATGGCCTAATtttttt                                                                                                      >  1:9688/1‑149 (MQ=255)                                                         cGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGGATGA‑AAGAAAAAACAAGCAATAATAT‑AATAATAGGCTAATTTTTTTGTACATCATTaa                                                                                          >  1:359938/1‑150 (MQ=255)                                                           aGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTTGTATTA‑AAAAAAAAAAAAACAAAAAAATAAAAAATGGCC‑AATTTTTTTTAAAATCATTaa                                                                                          >  2:61327/1‑148 (MQ=255)                                                                 cTTTCCTGATTATAACTCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGTTATGA‑CAAAAAAACCAAGCCAAAAAAT‑AATAAATGCCTCATTTTTTTTAAca                                                                                                 >  2:198707/1‑135 (MQ=255)                                                                 cTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGAATGA‑AAAAAAAAGGAAACAAAAATAT‑AAAAAATGGCTTATTTTTTTTAAAATCATTaaaaaaaaca                                                                                  >  1:587055/1‑142 (MQ=255)                                                                                 tCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGTTTTTTGAATGA‑AAAAAAATACAAGAAAAAATAT‑AATAAAAGCCTAATTTTTTTTAACAACATTAAACATATTATCATCCTCTATTTTcc                                                                  >  1:409381/1‑150 (MQ=255)                                                                                   ttATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGAATGA‑AAAAAAAAGCAAACAAAAAAAT‑AATAAAAGCCTAAATTTTTTTAAAAACATTAAACATATTATCATCGTCTAtttttca                                                                 >  1:493036/1‑145 (MQ=255)                                                                                        gTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCg                                                          <  2:393819/151‑1 (MQ=255)                                                                                                       ttCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGGATGA‑AAAAAAAAGGAAACAAAAAAAT‑AAAAAATGGCTAATTTTTTTTTAAATCATTTAAAATATCATCATCGTCTATTTTTCAGAAACCGTCGACTTATAAtttc                                           >  1:329871/1‑148 (MQ=255)                                                                                                        tCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGGGTGA‑AAGAAAAAGCAAACAATAATATAAAAAATGGCC‑AATTTTTTTTTAAATCATTAAACATATCATTCTTGTCTATTTTTCAGAAACCGTCGGCTTTTAAttccc                                          >  1:68408/1‑147 (MQ=255)                                                                                                         ccTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGAATGA‑AAAAAAAAGGAAGCAAAAATAT‑AAAAAAGGCCTAATTTTTTTTTACATCATTAAACATAACATCATCCTCTTTTTTCCCGAAAACGTCCACTTATAAttacc                                          >  1:444220/1‑146 (MQ=255)                                                                                                              gCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGAATGA‑AAAAAAATTAAAGCGATAAAAT‑AATAAAGGGCTAATTTCTTTTAAAATCATTAAACAAATAATCATACTTTAtttttcatca                                                              >  2:708546/1‑118 (MQ=255)                                                                                                              gCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAAc                                     <  2:382429/150‑1 (MQ=255)                                                                                                              gCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAAGCGCCAGAAc                                     <  2:464870/150‑1 (MQ=255)                                                                                                               cATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTGGGATGA‑AAAAAAAAGCAAACAATAAAAA‑AAAAAATGGCTAATTTTTTTTAAAATCATTAAACAAATCATCATCGTCTATTTTTCAGAATCCGTCGACTTATAAACGCCAGAAAgg                                   >  1:219284/1‑151 (MQ=255)                                                                                                                aTAATGCGCCTGGGATTAATGGCGGGGGGTTTTTGGGATGA‑AAAAAAAAACAAACAAAAATAT‑AAAAAAAGGCTAATTTTTTTTAAAATAATTAAAGATATCATTATCGTCTTTTTTTCAGAAACCGTCGACTTATAATTGCCAGAACgg                                   >  1:465322/1‑150 (MQ=255)                                                                                                                 tAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGGAAGA‑AAAAAAAAGGAAGCAAAAATAT‑AATAAAAGCCTAATTTTTTTTAACAACATTAAAAATATCATCATCGTCTATTTTCCAGAATACGTCGACTTATAATCGCCAGAAAgg                                   >  1:520002/1‑149 (MQ=255)                                                                                                                 tAATGCGCCTGGGATTAATGGCGGGGGCTTTTTGGGAAAA‑AAAAAAAAGAAAACAAAAAAAT‑AAAAATGGGCTCAATTTTTTGAAAAACATTAAAAAGAACATCAATGTCTATTTTCCAGAAATCGCCGACATATAAACTCCAAAAAGGc                                  >  1:225217/1‑150 (MQ=255)                                                                                                                  aaTGCGCCTGGGATTAATGGCGGGGGGTTTTTTGGAAGA‑AAAAAAAAACAAACAAAAAAAT‑AAAAAAAGACTAATTTTTTTTTAAATCATTTAAAAAATCATCATCGTCTATTTTTCAGAAACCCTCGACTTATAATCTCCCGaa                                      >  1:142168/1‑145 (MQ=255)                                                                                                                                 aaTGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGtgctg                 <  1:673785/151‑1 (MQ=255)                                                                                                                                      cGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAAc            <  2:558144/151‑1 (MQ=255)                                                                                                                                       gggTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACg           <  1:713837/151‑1 (MQ=255)                                                                                                                                       gggTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTCCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCCTATCAGGACGGTGCTGCGAAc            <  2:158224/150‑1 (MQ=255)                                                                                                                                        ggTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGc          >  1:72217/1‑151 (MQ=255)                                                                                                                                         gTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCTTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCt         <  2:335945/151‑1 (MQ=255)                                                                                                                                             ttttAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTgg     >  1:584267/1‑151 (MQ=255)                                                                                                                                              tttAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCtgtg      <  2:240313/149‑1 (MQ=255)                                                                                                                                              tttAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGc    >  2:569202/1‑151 (MQ=255)                                                                                                                                                tAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATAACAGGACGGTGCTGCGAACGCTGTGGcc   <  2:142155/150‑1 (MQ=255)                                                                                                                                                 aGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGccc  >  1:423546/1‑150 (MQ=255)                                                                                                                                                 aGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGccc  >  1:647061/1‑150 (MQ=255)                                                                                                                                                 |                                                                                                                                                        ACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGA‑AAGAAAATGCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCC  >  NC_000913/4536053‑4536346

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑