Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	49.0%	46.7 / 30.8	51	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (23/3);  new base C (0/25);  total (23/28)
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

TTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCG  >  NC_000913/1376358‑1376654                                                                                                                                                       |                                                                                                                                                      ttACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACAccc                                                                                                                                                    >  1:456523/1‑151 (MQ=255)     cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGc                                                                                                                                                >  2:168555/1‑151 (MQ=255)         gATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGAt                                                                                                                                            <  2:491928/151‑1 (MQ=255)                  gccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGt                                                                                                                                   >  2:629324/1‑151 (MQ=255)                   ccgcGTAGCCTGGACGGCGACCGCAAAAGGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACCCCCTCGCCGATGCccgccg                                                                                                                                    <  1:530310/149‑1 (MQ=255)                       gTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAt                                                                                                                              >  2:570835/1‑151 (MQ=255)                           ccTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtcgtc                                                                                                                          >  1:294008/1‑151 (MQ=255)                             tGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGACCAGGTC‑GCCGCGCGTACCGGAACCGTGGTGCATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCTCCGCTACAtcgtcg                                                                                                                         >  1:322904/1‑150 (MQ=255)                               gACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGaa                                                                                                                       >  1:651779/1‑150 (MQ=255)                                 cGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAAc                                                                                                                    >  1:560539/1‑151 (MQ=255)                                  ggCGCCCGCAAGATGGTGAGTGTTCCCCGGCGCGTGTGGAAACGGGTC‑GCCGCCCGTACCGAAAGGGTGGTTTATCCCGACCCGTAAAC‑CCGCTTT‑CAGGTTCATAGGACAAACACCCGCGCCAGTCCCCGCCGTTACATCGTCGAAAAc                                                                                                                    <  1:107512/150‑1 (MQ=255)                                  ggCGCCCGAAAAAGGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTCCCGGACCCGGGGTGTATCTCAACCCTTTAAC‑CCGCTAT‑AAGGATCATATGATCAACCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACg                                                                                                                   <  2:178425/151‑1 (MQ=255)                                    cGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGAC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGAt                                                                                                                 >  2:204843/1‑151 (MQ=255)                                       ccGCAAATGGGGGGGTGTTCCCCTGCGCGTCCGGGAACAGGTC‑GCCGGGCGTCCCGAACCGGTGGTGTATCCCGAACCTTAAAC‑CCGCTAT‑CAGTATAATATAATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                              <  1:681100/151‑1 (MQ=255)                                           aaaaTGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAAc                                                                                                          >  2:465226/1‑151 (MQ=255)                                               gggggagtgaTCCCCGGCGGGTACTGAAACGGGCC‑GCGGCGCGTCCGGGACCCGGGGTGTATCGCAAACCGTAAAC‑CCCCTAC‑AAGAATCATATGAAAACCCCCCCCGCGGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGt                                                                                                      <  2:167228/147‑1 (MQ=255)                                                ggTGAGTGTTCCCCTGCGCTTAAGGGAACAGCTC‑CCCGCGCGCACCGGACCCGTGGTGTATCTCGACCCGTTAAC‑CCGCTAT‑CGGTATCATATACCCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTa                                                                                                     <  1:186245/151‑1 (MQ=255)                                                     gtgaTTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                                    >  2:545322/1‑147 (MQ=255)                                                         ttCCCTGGGCTTAC‑GGAAACGGTCGGCCGGCCGTCCGGGAACCGGGGTGTTTC‑CCAACCCTTAAACCCTCTAA‑AAGGATAATATGATCAACCCCCCCGCCTAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                             <  1:640977/150‑1 (MQ=255)                                                           ccgtGCGGGTCCGGGAAGAGGCC‑GCGCCGCTAACCGGACCCGTGGTTTACCCCG‑ACCCTTAAA‑CCCCTTTACGGGATAAAATACTCACCCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAt                                                                                                <  1:221757/142‑1 (MQ=255)                                                                 gcgTCCTGAAACAGGCC‑CCCGCCCGACCCGGACCGGGGGTTTATC‑CCAACCGTTAAACCCCCTAT‑CAGGATAATATAACCAACCCCCTCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                                    <  1:658542/151‑1 (MQ=255)                                                                       gggAACGGGTC‑GCCGCGGTTCCCGGACCCGTGGTTTACCCCGACCCGTAAAC‑CCCCTAT‑CAGGATAATATAACCACCCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATca                                                                              <  1:444228/150‑1 (MQ=255)                                                                        ggAACAGGTC‑GCCGCGCGTCCCGAAACCGCGGTGTATCTCAACCCGTTAAC‑CCCCTAT‑CAGGATAATATGATCACCACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATca                                                                              <  1:115324/150‑1 (MQ=255)                                                                        gaaaCAGGTC‑GCCGCGCGTCCCGGACCCGTGGTGTATCTCGACCCGTTAAA‑CCGCTAT‑CAGGATCATATGATAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                               <  2:169603/147‑1 (MQ=255)                                                                        gaaaCAGGTC‑GCCGCGCGTCCCGGAACCGTGGTGTATCTCGAACCGTAAAA‑CCGCTAT‑CAGGATAATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcac                                                                             <  2:307380/149‑1 (MQ=255)                                                                         gAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcac                                                                             >  1:710438/1‑150 (MQ=255)                                                                                    ccgcGCGTACCGGAACCGTGGTGTATCTCGAACCTTTAAC‑CCGCTAT‑CAGGATCATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGa                                                                         <  2:49773/144‑1 (MQ=255)                                                                                          gTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                               >  2:636372/1‑148 (MQ=255)                                                                                             ccGGACCTGTGGTGTCTCTCGAACCTTTAAA‑CCGGTAT‑CAGTATCATATGACCAACCCCCCCGCCCATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGACGATTTCTATCACATGAATATCGAAGAAGATa                                                          <  1:441302/150‑1 (MQ=255)                                                                                             ccGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATa                                                          >  1:665123/1‑150 (MQ=255)                                                                                             ccGAAACCGTGGTGTATCTCAACCCGTTAAC‑CCGCTAT‑CAGAATAATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGAt                                                           <  2:422939/149‑1 (MQ=255)                                                                                               ggACCCGTGGTTTATCCCAACCCGTAAAC‑CCCCTAT‑CAGGATCATATGACAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                         <  2:382955/149‑1 (MQ=255)                                                                                               ggAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                                       >  2:711141/1‑151 (MQ=255)                                                                                                 accggtggtgTA‑CCCCAACCTTTAAACCCGTTAA‑CAGTATAATATAAACAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAc                                                        <  1:423477/144‑1 (MQ=255)                                                                                                   cggtggtgTATCTCAACCCTTTAAC‑CCGCTAA‑CAGGATCATATGACCACCCCCCTCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                                     <  1:83962/147‑1 (MQ=255)                                                                                                         tgtATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgc                                             >  2:120104/1‑151 (MQ=255)                                                                                                         tgtACCTCGACCCTTAAAC‑CCGCTAT‑CAGGATAATATGATCACCCCCCTCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAg                                               <  2:551225/149‑1 (MQ=255)                                                                                                             tctcGACCCTTTAAC‑CCGCTAT‑CAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGGGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCt                                          <  2:203747/150‑1 (MQ=255)                                                                                                                cGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGGCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGGATATCGAAGAAGATAACCTGGCGCAGGCGCTgaa                                       >  1:565624/1‑148 (MQ=255)                                                                                                                   aactttAAACCCGCAAT‑AAGGTTAATAGAATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCAt                                      <  1:210126/145‑1 (MQ=255)                                                                                                                          aacccccTAT‑CAGAACCATATAACAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAcc                               <  1:698709/143‑1 (MQ=255)                                                                                                                             ccGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAc                          >  2:150672/1‑151 (MQ=255)                                                                                                                              cgtctctgaGGAACATAGGACCACCCCCCGCGCGGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAc                                <  1:567003/137‑1 (MQ=255)                                                                                                                                         aTCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTc                >  1:538404/1‑150 (MQ=255)                                                                                                                                           cATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg             >  2:274399/1‑151 (MQ=255)                                                                                                                                            atatGACCACCCCCCCCGCCGACGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAt              <  1:168513/149‑1 (MQ=255)                                                                                                                                            atatGACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg             <  2:123646/150‑1 (MQ=255)                                                                                                                                              atGATAAACCCCCTCCCCTAGGACCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtgtg           <  2:366692/150‑1 (MQ=255)                                                                                                                                                  tCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTCCAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCata       >  1:388713/1‑150 (MQ=255)                                                                                                                                                   cAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGCAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGCGCAGGTGCa         >  1:359056/1‑147 (MQ=255)                                                                                                                                                   cAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATAtt     >  2:55967/1‑151 (MQ=255)                                                                                                                                                     acacCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGc   >  2:580521/1‑151 (MQ=255)                                                                                                                                                     acacCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGc   >  1:693132/1‑151 (MQ=255)                                                                                                                                                     acacCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGc   >  1:585830/1‑151 (MQ=255)                                                                                                                                                      cacCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCg  >  2:275052/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                      TTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTC‑GCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTAT‑CAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCG  >  NC_000913/1376358‑1376654

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑