Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,573,500	0	A	G	42.3%	78.8 / 14.7	52	pseudogene (1087/1503 nt)	yjiT	pseudogene
Reads supporting (aligned to +/- strand):  ref base A (2/28);  new base G (22/0);  total (24/28)
Fisher's exact test for biased strand distribution p-value = 1.02e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCCCTCGG  >  NC_000913/4573355‑4573649                                                                                                                                                   |                                                                                                                                                          aGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑GGGTGGGGGGGTGAtt                                                                                                                                                      >  1:806897/1‑151 (MQ=255)  gATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGGGGGGTGAtt                                                                                                                                                      >  1:284666/1‑150 (MQ=255)     ggTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGAttgtt                                                                                                                                                   <  2:465207/150‑1 (MQ=255)           gAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGGTGGGGGGGAGGTTGTTtgggg                                                                                                                                              >  2:124970/1‑147 (MQ=255)           gAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGGGGGGTGATTGTTGGGAg                                                                                                                                              >  1:680722/1‑149 (MQ=255)           gAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑GGCGGGAGGGGGGGTTGTGGGGAg                                                                                                                                              >  2:20441/1‑149 (MQ=255)             aGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCAtt                                                                                                                                          <  1:479950/151‑1 (MQ=255)                  ctGGCCTTGGGTCAGCCTATGCTTCTCTGGAAAACAGACAGGCATCAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGGAGGCAAAATCCATCGGCATGTTTGTCTTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGCGCATTaaa                                                                                                                                       <  2:534146/149‑1 (MQ=255)                  ctGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGGGGGGTGATTGTTTGGAGGATTtaa                                                                                                                                       >  1:337670/1‑149 (MQ=255)                  ctGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTaaa                                                                                                                                       <  1:823867/149‑1 (MQ=255)                            gCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGGGGGGTGAATGTTGGGGGCATTAAAATTGGTGACa                                                                                                                             >  1:467306/1‑149 (MQ=255)                             ccAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCCGGAGGGATGATTGTTGGGGGGATTAAACTtgat                                                                                                                                 >  1:725760/1‑144 (MQ=255)                               aGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑aa                                                                                                                       <  1:395436/151‑1 (MQ=255)                                    aTGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGc                                                                                                                 <  1:104740/151‑1 (MQ=255)                                        ttCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGGTGGGGGGGTGGTTTTTTGGGGCATTAAACTTGATGACAGGG‑aaaattccctt                                                                                                              >  1:666130/1‑143 (MQ=255)                                         tctcTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑Att                                                                                                            <  1:378903/150‑1 (MQ=255)                                         tctcTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑Att                                                                                                            <  1:204002/150‑1 (MQ=255)                                              ggAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGt                                                                                                         <  2:447034/148‑1 (MQ=255)                                               gAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAgg                                                                                                     <  2:640872/151‑1 (MQ=255)                                                    cagacagGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCg                                                                                                <  1:624711/151‑1 (MQ=255)                                                        cagGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGGTTGTCGTTAGTGGCCCG‑TGGTGGGGGGGGGGTTGTTGGGGGTATTAAACTTTATAACAAAG‑AAA‑ATGCG‑ATTTGTGAGGGGTCGtt                                                                                              >  1:472147/1‑149 (MQ=255)                                                            cAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGGTGGGGGGGTGGTTGTTGGGGGGATTTAACTTTTTGAAAGTG‑GAA‑ATGCC‑CTTGGTGGGGGGGCGTTTACCtt                                                                                        >  2:590184/1‑151 (MQ=255)                                                             aaCAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTc                                                                                       <  1:598002/151‑1 (MQ=255)                                                              aCAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑GGGTGGAGGGGAGGTTGTTTGGGGCATTAAAATTTATGGAAAGG‑AAA‑ATGGC‑ATTTGTGGGGTGGCGTTAAccct                                                                                        >  1:152788/1‑147 (MQ=255)                                                                 gTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCg                                                                                   <  2:280792/151‑1 (MQ=255)                                                                         aCGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCa                                                                           <  1:675746/151‑1 (MQ=255)                                                                             aaaaGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGAt                                                                        <  1:788612/150‑1 (MQ=255)                                                                             aaaaGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATc                                                                       <  1:511116/151‑1 (MQ=255)                                                                                aGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGGGGGGTGATTGTTGGGGGGATTTAACTTGATGACAGTG‑AAA‑TTGCC‑CTTGGTGAGGGGCCGTTAAACTTCATCGTTGATGCAGATCaa                                                                     >  1:264367/1‑150 (MQ=255)                                                                                    aaGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGGTGGGGGGGAGATTGTTTGGGGGATTTAACTTGGTTGCAGGG‑GAA‑TTGCCAATGGGGGGGGGGCCGTTAACCTTC‑TCCGTGATGCAGa                                                                         >  2:431002/1‑142 (MQ=255)                                                                                      gTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGGGGGGTGATTGTTGGGGGCATTTAAATTGATGGAAGTG‑AAA‑TTGCC‑ATTGGGGGGGGGCCGTTAACCTTCATCGTTTATGCAGATCAATgg                                                                  >  1:814385/1‑147 (MQ=255)                                                                                        gagaTTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGtt                                                            <  2:860021/150‑1 (MQ=255)                                                                                          gaTTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGGGGGGTGATTGTTGGGAGGATTAAAATTGATGACAGTG‑AAA‑TTGCC‑ATTGGGGAGGGGCCGGTAACCTTCATCGGTGATGCAGATCAATTG‑CTGtt                                                            >  1:641894/1‑148 (MQ=255)                                                                                           aTTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑GGGTGGGGGGGTGGTTGTTGGGGGCATTAAAATTGATGACAGTG‑AAA‑TTGCC‑CTTTGGGGGGGGGCGGTAACCTTCCTCGTTTGTGCAGATCAATGG‑GTggt                                                            >  1:292385/1‑145 (MQ=255)                                                                                              tGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAggg                                                      <  1:461512/150‑1 (MQ=255)                                                                                              tGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCCCGTTGCTGG‑GGGGTGATTTTTGGGGGGATTTAACTTTGTGGCAATG‑GAA‑TTTCC‑ATTGGTGGGGGGGCGGTTAACTTCCTCGGTGATGTGGAACAATTG‑GTGTTTCAagg                                                      >  2:6362/1‑150 (MQ=255)                                                                                                  aggcaAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑GGCTTGGGGGGAGATTTTTGGGGGGATTTTACTTTGTGACAAGG‑AAATTTGCC‑TTTGG‑GGGGTGCCGTTTACCCTTCTCGTTTATGCAGATCCATTG‑GTGGTTTAGGGGCAgg                                                 >  2:831058/1‑151 (MQ=255)                                                                                                    gcaAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGct                                               <  2:327978/151‑1 (MQ=255)                                                                                                      aaaaTCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGcttc                                             <  2:82536/151‑1 (MQ=255)                                                                                                       aaaTCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGcttct                                            <  2:221098/151‑1 (MQ=255)                                                                                                        aaTCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGGTGATTGTTGGGGGCATTAAACTTGGTGACAGGG‑AAA‑ATGCC‑ATTTGGGGGGGGCCGTTAACCTTTATCGTTGATGCAGATCAATGG‑CTGTTTCAAGGGCAGGcttttt                                           >  1:587798/1‑151 (MQ=255)                                                                                                        aaTCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑GGCTGGGGGGGTTATTTTTGGGGGGATTTAACTTTATGACAGGGAAAA‑TTGCC‑‑TTGGTGGGGGGGCGTTTAACTTCATCGTTGATGGAGATCAATGGCCTGTTAAGGGGAAAGGttttt                                            >  2:157344/1‑149 (MQ=255)                                                                                                            cATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTGCAg                                       <  1:798850/151‑1 (MQ=255)                                                                                                                ggCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGGGGGACGATTGTTGGGAGCCTTTAAATTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGGGCCGTTAACCTTTATCGTTTATGCAGATCAAAGG‑CTGTTACAGGGAGAGGCCTCTTGCAGtgtg                                   >  2:206675/1‑151 (MQ=255)                                                                                                                 gCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTGCAGTGTGc                                  <  2:770587/151‑1 (MQ=255)                                                                                                                  cAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGGTGATTGTTTGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGGGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTTCAGtgtg                                   >  2:609840/1‑149 (MQ=255)                                                                                                                     gTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAag                              <  2:18642/151‑1 (MQ=255)                                                                                                                     gTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAag                              <  1:521957/151‑1 (MQ=255)                                                                                                                      tttGTCGTTAGTGGCTCG‑TGCTGGAGGGGTGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAag                              >  1:219854/1‑150 (MQ=255)                                                                                                                         gTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAagcagc                          <  2:468142/151‑1 (MQ=255)                                                                                                                                              gAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTccc      <  1:640650/151‑1 (MQ=255)                                                                                                                                                gggATGATTGTTGGGAGCATTAAACTTGATGACAAGG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGAGGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGTGATGTTCTGATTGTGCTccc      <  2:325121/149‑1 (MQ=255)                                                                                                                                                  gatgatTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCCCTCgg  <  2:829427/151‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                          AGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCG‑TGCTGGAGGGATGATTGTTGGGAGCATTAAACTTGATGACAGTG‑AAA‑TTGCC‑ATTGGTGAGGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGG‑CTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCCCTCGG  >  NC_000913/4573355‑4573649

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑