Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	51.8%	53.4 / 98.7	56	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (23/4);  new base C (0/29);  total (23/33)
Fisher's exact test for biased strand distribution p-value = 5.54e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.69e-09

CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATG  >  NC_000913/1376357‑1376643                                                                                                                                                          |                                                                                                                                           cTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACAcc                                                                                                                                          >  1:361316/1‑151 (MQ=255)    aCCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACAcc                                                                                                                                          <  1:26096/148‑1 (MQ=255)     ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCg                                                                                                                                      <  2:462597/151‑1 (MQ=255)      cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGc                                                                                                                                     >  2:1071343/1‑151 (MQ=255)        ccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCg                                                                                                                                   <  1:909360/151‑1 (MQ=255)             gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGcc                                                                                                                              >  1:847729/1‑151 (MQ=255)               ccTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCccg                                                                                                                            <  1:2581/151‑1 (MQ=255)                   gccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGt                                                                                                                        >  2:826384/1‑151 (MQ=255)                             cTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtcgtcg                                                                                                              >  1:48520/1‑151 (MQ=255)                                gACGGCGACCGCAAAATGGTGAGCGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGaa                                                                                                            >  1:651116/1‑150 (MQ=255)                                   gccGACCGAAAAAGGGTGAGTGATCCCCTGCTCTTACGGAAACG‑GGTCGCCGCG‑GTTCCGGAAACCGTGTTGTATCTCGACCCGTAAA‑C‑CCTCTATCGGGAT‑CATATGATAACCCCCCTCGCCGATGCCCGCCGTTACAtc                                                                                                                  <  1:906392/139‑1 (MQ=255)                                      gcccGAAAAAGGGTGAGTGATTCCCTGCGCTTCTTGAAACA‑GGTCGCCGGGCGTACCGG‑ACCCGGGGTTTATCTC‑AACCCTTAA‑ACCCGTTAACAGGAT‑TATATAAACAACCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGa                                                                                                       <  2:787142/147‑1 (MQ=255)                                        ccGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATc                                                                                                     >  2:10771/1‑149 (MQ=255)                                        ccGCAAAATGGTGAGTGATCCCTGGCGGTTCCTGCAACA‑GGCCGCCGGGCGGACCGA‑ACCCGTGGTGTATCTCGAACCGTAAA‑C‑CCGCTATCGGGAT‑CATATGATCACCCCCCGCGCCGGTGCCCGCCGTTACATCGTCGAAAACGATc                                                                                                     <  2:180621/149‑1 (MQ=255)                                        ccGAAAAAGGGGGAGTGATTCCCGGCGCGTCCTGGAACG‑GGTCGCCGCGCGTCCCGG‑ACCCGTGGTGTATCTCGACCCTTTAA‑C‑CCGCTACCAGGAT‑CATAGGAACAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGAt                                                                                                      <  2:727744/148‑1 (MQ=255)                                           cAAAGTGGGGGGTGTTTCCCGGCTAGTCCGGAAACG‑GGTCGCCGCGTGACCCGG‑AACGGTGGTTTTCCACGACCCGTTAA‑T‑CCGATCCCGGCTT‑CTTATGACAACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCt                                                                                                    <  2:153368/147‑1 (MQ=255)                                            aaaaTGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAAc                                                                                               >  1:687819/1‑151 (MQ=255)                                                 ggggggtgaTTCCCTGCGGGTTCGGGAACG‑GGTCGCCGCGCGTACCGG‑AACCGGGTTATACCCCTAACCGTAAA‑C‑CCCCTATCAGGAT‑AATATGACCACCCCCCTCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATg                                                                                            <  1:283315/144‑1 (MQ=255)                                                    gagtgaTTCCCTGCGCGTACTGGAACG‑GGTCGCCGCGCGTACCGG‑ACCCGTGGTGTATCTCGACCCTTTAA‑C‑CCGCTATCAGGAT‑CATATGATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAg                                                                                       <  2:256997/151‑1 (MQ=255)                                                    gagtaaTCCCCGGCGTGTAC‑GGAACAGGGAGGCCGCGCGCCCCGG‑ACCGGTGGTGTATCTCGAACCTTTAA‑C‑CCTCTATCACTAT‑CATATAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACa                                                                                        <  1:963928/150‑1 (MQ=255)                                                      gtgttccccTGCGGGTA‑TGGAACAGGGTCGCCGCGCTTCCCGG‑ACCGGTGGTTTATCTC‑AACCCTTAA‑ACCCGCTATAAGAAT‑AATATGATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACa                                                                                        <  1:870377/142‑1 (MQ=255)                                                          tccccTGCGCGTCCGGAACCA‑GGCCGCCGCGCGTCCCGA‑ACCGGTGTTGTATCTCGACCCTTAAA‑C‑CCGCTATCAGAAT‑CATAAAACCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                  <  1:970098/148‑1 (MQ=255)                                                            cccTGCGCGTCCTGGACCG‑GGTCGCCGCGCTTCCCGG‑ACCCGTGTTGTATCTCAACCCGTAAA‑C‑CCGCTATCAGAAT‑AATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATc                                                                                 <  2:441016/149‑1 (MQ=255)                                                                  gcgTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                         >  1:129428/1‑151 (MQ=255)                                                                  gcgTACGGAAACG‑GTTCCCCGCCCTTCCGGG‑ACCGGGGGTGTTTCTCGACCCTTAAA‑C‑CCGCTATCAGGAT‑AATATGACCAACCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAtt                                                                          <  2:1044460/150‑1 (MQ=255)                                                                   cgTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTc                                                                        >  1:1067649/1‑151 (MQ=255)                                                                     tACTGAAACG‑GGTCGCGGCGCGTCCCGG‑ACCGGTGGTTTTTC‑CGAAACGGTAACC‑CCGCTATCAGGAT‑CATATAATAACCCCCCCCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                         <  1:462149/148‑1 (MQ=255)                                                                      aggggAACA‑GGCCGCCGCGCGTACCGG‑AACGGTGGTGTATCTCGAACCTTAAA‑C‑CCGCTAACAGTAT‑CATATGATCAACCCCCCCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTa                                                                      <  1:785032/147‑1 (MQ=255)                                                                         ggAACA‑GGTCGCCGCGCGTACCGG‑ACCGGTGGTGTATCTCGAACCGTTAA‑C‑CCGCTATCAGGAT‑CATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATca                                                                   <  2:454039/150‑1 (MQ=255)                                                                                ggTCCCCGCGCTCCCCGA‑AACTGTGGTTTACCCAGACCCTTTAA‑C‑CCGCT‑TAAAGATACATATAAACACCCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcaca                                                                 <  2:944000/146‑1 (MQ=255)                                                                                             aCCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGAt                                                >  2:632840/1‑150 (MQ=255)                                                                                                gg‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                            >  1:751774/1‑151 (MQ=255)                                                                                                   accgggggtgTATCCCAACCCGTAAA‑C‑CCGCTATCAGAAC‑CATATGAAAACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                          <  2:734865/145‑1 (MQ=255)                                                                                                   aaCCGTGGTTTATCTCGACCCGTTAA‑C‑CCGCTATCAGGAT‑CATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCt                                           <  2:393562/150‑1 (MQ=255)                                                                                                       gtggttTATCTCAACCCGTAAA‑C‑CCGCTATCAGGAT‑AATATGAACACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                         <  2:847854/148‑1 (MQ=255)                                                                                                         ggttTATCGCGAACCTTTAA‑C‑CCGCTATCAGGAT‑CATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAg                                    <  2:499587/151‑1 (MQ=255)                                                                                                         ggtgTATCTCGACCCTTTAA‑C‑CCGCTATCAGGAT‑AATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                         <  2:765662/146‑1 (MQ=255)                                                                                                         ggtgTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcgc                                      >  1:244946/1‑149 (MQ=255)                                                                                                         ggtgTATCTCAAACCTTAAA‑C‑CCGTTATCAGAAT‑CATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAg                                    <  2:850603/151‑1 (MQ=255)                                                                                                           tttttctaaaccctttAA‑C‑CCGTTATCAGAAT‑AAAATGATAACCCCCCGCGCCGTGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAgg                                   <  1:1076071/136‑1 (MQ=255)                                                                                                             tATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgcgc                                >  1:1033270/1‑151 (MQ=255)                                                                                                             tATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgcgc                                >  2:215872/1‑151 (MQ=255)                                                                                                                ctcGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGc                             >  2:489105/1‑151 (MQ=255)                                                                                                                  ccgaCCCTTAA‑ACCCGTTATCAGAAT‑CATATGAACAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCa                            <  1:891903/148‑1 (MQ=255)                                                                                                                  cGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCa                            >  1:199390/1‑150 (MQ=255)                                                                                                                  cGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCAt                           >  1:80319/1‑151 (MQ=255)                                                                                                                   gAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATg                          >  2:443632/1‑151 (MQ=255)                                                                                                                    accctttAA‑A‑CCGCTATCAGGAT‑CATATGATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCt                               <  1:510813/140‑1 (MQ=255)                                                                                                                     aCCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGAc                        >  1:167244/1‑151 (MQ=255)                                                                                                                         ttAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAcc                    >  2:1048019/1‑151 (MQ=255)                                                                                                                          tAA‑A‑CCGCTATAAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAcc                    >  1:1012417/1‑150 (MQ=255)                                                                                                                           aa‑a‑CCGCTATCGGGAT‑CATATGACCAACCCCCCCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgc                  <  2:395083/151‑1 (MQ=255)                                                                                                                                      aaaGGAT‑AATATGACCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTc         <  1:120325/149‑1 (MQ=255)                                                                                                                                              cATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg  >  1:228447/1‑151 (MQ=255)                                                                                                                                                tatGAACAACCCCCCCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg  <  2:188836/149‑1 (MQ=255)                                                                                                                                                    aTCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCa    <  2:278668/143‑1 (MQ=255)                                                                                                                                                          |                                                                                                                                           CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACA‑GGTCGCCGCGCGTACCGG‑AACCGTGGTGTATCTCGAACCGTTAA‑A‑CCGCTATCAGGAT‑CATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATG  >  NC_000913/1376357‑1376643

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑