Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,536,197	0	A	T	41.2%	64.1 / 36.7	51	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 (5/25);  new base T (21/0);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 6.85e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCC  >  NC_000913/4536054‑4536345                                                                                                                                                  |                                                                                                                                                       cAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATga                                                                                                                                                 <  2:543800/151‑1 (MQ=255)  aGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATgaa                                                                                                                                                <  1:1007921/151‑1 (MQ=255)    gAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATgaaag                                                                                                                                              <  1:109971/151‑1 (MQ=255)    gAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATgaaag                                                                                                                                              <  2:820604/151‑1 (MQ=255)        agtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATgaaagaaa                                                                                                                                           <  1:359414/150‑1 (MQ=255)           aaaGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGG‑GG‑TTTTTTGGATGAAAGaaaa                                                                                                                                          >  2:535583/1‑148 (MQ=255)                 cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑gcaagcaa                                                                                                                                <  2:274228/151‑1 (MQ=255)                        tACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GG‑TTTTTGGAATGAAAAAAAAA‑GCAAGCAaaaatat                                                                                                                          >  1:872718/1‑150 (MQ=255)                         aCCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAataatat‑a                                                                                                                        <  2:919228/150‑1 (MQ=255)                           cAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAAtaatat‑aata                                                                                                                     <  2:477668/151‑1 (MQ=255)                            aaTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGATGGT‑TTTTTGGAAT‑AAAGaaaaaagaaaaaaaaata                                                                                                                            >  2:24211/1‑131 (MQ=255)                                 tAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGc                                                                                                                <  1:355306/150‑1 (MQ=255)                                   aGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTa                                                                                                             <  2:614453/151‑1 (MQ=255)                                      cGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GG‑TTTTTTGATTTAAAAAAAAA‑AAAAGCaata                                                                                                                              >  2:659255/1‑132 (MQ=255)                                      cGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAAtt                                                                                                          <  2:1095029/151‑1 (MQ=255)                                      cGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAAtt                                                                                                          <  2:857526/151‑1 (MQ=255)                                            tCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCttt                                                                                                     <  2:514702/150‑1 (MQ=255)                                             ccGTTTTATTGCGAGTCGCCTTTCATGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGA‑GC‑TTTTTTGGATTAAAAAAAAA‑GCAAGCAAAAAAAT‑AATAAAGGCATAAAtttttt                                                                                                     >  2:432696/1‑149 (MQ=255)                                               gTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTTTTGATGAAAGAAAAA‑AACAGCCAAAATATAAAAAATGGCTTAttttttttt                                                                                                    >  2:626330/1‑148 (MQ=255)                                                    aTTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAAcatca                                                                                             <  1:1087627/150‑1 (MQ=255)                                                      tGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGG‑GG‑GTTTTGGGATGAAAAAAAAA‑ATAAGGCATAAAAT‑AATAAAAGCCCAATTTCtttttaaat                                                                                               >  1:394047/1‑140 (MQ=255)                                                       gCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTaa                                                                                         <  2:255215/151‑1 (MQ=255)                                                        cGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAg                                                                                        <  1:624034/151‑1 (MQ=255)                                                        cGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATATTCCTTTGCATAATGCGCATGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAAcatcat                                                                                            <  2:871313/147‑1 (MQ=255)                                                               ccTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATatca                                                                                 <  1:555595/151‑1 (MQ=255)                                                                 tttCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GG‑TTTTTGGGAAGAAAAAAAAA‑GCAAACAATAATAA‑AATAATAGCCTAATTTTTTTTAACAACATTAAACata                                                                                    >  1:891158/1‑146 (MQ=255)                                                                 tttCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GG‑GTTTTGGAATGAAAAAAAAA‑GAAAACAATAATAT‑AAAAAAAGCCTAATTTTTTTTTACATCAtttaagata                                                                                    >  1:257058/1‑139 (MQ=255)                                                                   tCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGG‑GC‑TTTTTTGAATGAAAAAAAAA‑GAAAACAAAAAAAT‑AATAAAAGGCTAATTTTTTTTAACAACATTAAACa                                                                                      >  1:1043018/1‑142 (MQ=255)                                                                    ccTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATatcatcat                                                                             <  2:242095/150‑1 (MQ=255)                                                                        aTTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTTTGAATGAAAGAAAAA‑GCAAACAATAAAAT‑AATAAATGCCTAATTTTTTTTAACATCATTAAACATATCATCATCctct                                                                        >  1:419765/1‑151 (MQ=255)                                                                           ataAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTAt                                                                      <  1:888902/150‑1 (MQ=255)                                                                             aaaTCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGG‑GC‑TTTTTTGGAAGAAAAAAAAA‑GGAAGCAAAAAAAT‑AAAAATGGGCTAATTTTTTTTAACATCATTAAGCAAATCATCATCGTCTAtttt                                                                   >  1:253475/1‑150 (MQ=255)                                                                                   tATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCa                                                                <  1:382354/148‑1 (MQ=255)                                                                                         ttACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGG‑GG‑TTTTTTGGATGGAAGAAAAA‑GCAAGAAATAATAT‑AAAAATTGGCTCATTTTTTTTTAAATCATTAAACATATTATTATCGTCTTTTTTTCAGaa                                                             >  2:453328/1‑145 (MQ=255)                                                                                             cTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGG‑GG‑TTTTTTGAATGAAAAAAAAA‑GCAAGCAAAAAAAT‑AATAAAGGGCTAATTTTTTTTTAAATAATTAAAAATATAATCATCGTCTATTTTTCAGAAACCGTCGACt                                                   >  2:854802/1‑151 (MQ=255)                                                                                               aaTCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGG‑GC‑TTTTTGGGAAGAGAGAAAATACCAACCAGTAA‑AT‑AATAAAGGGCTTAATTTTTTTAAAAACATTAAACATATTATCATTCTCTATTTTCCTGAATCCCTCGACtt                                                  >  1:923224/1‑150 (MQ=255)                                                                                                aTCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GG‑TTTTTGGAATGAAAGAAAAA‑GAAAAAAAAAATAT‑AAAAAAAGGCTAATTTTTTTTTAAATAATTAAAAATATAATTATTGTCTATTTTTCAGAAACCCTCGACtt                                                  >  1:78304/1‑149 (MQ=255)                                                                                                  cATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTTTGAATGAAAAAAAAA‑ACAAACAAAAAAAT‑AAAAAAAGCCTAATTTTTTTTTACATAATTAAGCATAACATTATCCTCTCTTTTCCAGAATACGTCGAAtt                                                  >  1:446249/1‑147 (MQ=255)                                                                                                   aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAAt                                             <  1:515579/151‑1 (MQ=255)                                                                                                   aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGG‑GCTTTTTTGTATTGAAAAAAAAG‑TCAAG‑AAAAATAT‑AAAAATGGGCGTATTTTTTTTTACATAATTAAAAATAAAAAAAACTTCTATTTTTCAGAAACCGTctc                                                     >  2:114953/1‑141 (MQ=255)                                                                                                    ttttCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTTGGAATGAAAAAAAAT‑ACAAGCAATAATAT‑AATAAAGGGCCAATTTCTTTGTACATCATTTAACAAATCATCATCGTCTTTTTTCCAGAATCCGTCGGCtt                                                  >  1:552011/1‑145 (MQ=255)                                                                                                     tttCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATc                                            <  2:822224/150‑1 (MQ=255)                                                                                                        ccTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCa                                        <  2:458773/151‑1 (MQ=255)                                                                                                         cTTTGCATAATGCGCCTGGGATTAATGGCGGGG‑GG‑TTTTTTGGATGAAAAAAAAA‑ACAAGCAATAAAAT‑AATAAAAGCCTAAATTTTTTTAAAATCATTAAACAAAACATCATCGTCTATTTTCCAGAAACCCTCGACTTATaaaatcc                                         >  1:683934/1‑144 (MQ=255)                                                                                                                 aaTGCGCCTGGGATTAATGGCGGGG‑CG‑TTTTTATAATGAAAAAAAAA‑ACAAGCAATAATAT‑AATAATGGCCTAATTTTTTTTGATATCATTTATAATAATATTATTTTCTATTTTTCAGAATCCTGCGACTTATAAtactcagcaaag                                  >  2:13467/1‑137 (MQ=255)                                                                                                                                     cGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAAc           <  1:463673/151‑1 (MQ=255)                                                                                                                                     cGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAAc           >  1:715200/1‑151 (MQ=255)                                                                                                                                        gT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCt        >  1:324189/1‑151 (MQ=255)                                                                                                                                         t‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCtg       >  1:759151/1‑151 (MQ=255)                                                                                                                                            c‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCtgtg     >  2:502943/1‑151 (MQ=255)                                                                                                                                                ttAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGcc  >  2:35365/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                       CAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGT‑GC‑TTTTAGGAATGAAAGAAAAT‑GCAAGCAATAATAT‑AATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCC  >  NC_000913/4536054‑4536345

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑