Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,573,500	0	A	G	51.0%	48.6 / 75.6	49	pseudogene (1087/1503 nt)	yjiT	pseudogene
Reads supporting (aligned to +/- strand):  ref base A (7/17);  new base G (25/0);  total (32/17)
Fisher's exact test for biased strand distribution p-value = 5.33e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.70e-09

GAAGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCCCT  >  NC_000913/4573353‑4573646                                                                                                                                                     |                                                                                                                                                       gAAGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGgatga                                                                                                                                                     <  2:988841/151‑1 (MQ=255)  aaGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGCGCT‑GGGGGgagg                                                                                                                                                      >  1:550007/1‑147 (MQ=255)   aGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGGTTGTCGTTAGTGGCTCGGGGT‑GGGGGGGTGGtt                                                                                                                                                   >  2:351086/1‑151 (MQ=255)     aTGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGGTGAtt                                                                                                                                                   >  1:746978/1‑149 (MQ=255)              aaGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGT‑GGGGGGGTGGTT‑TTTtgg                                                                                                                                            >  2:5339/1‑146 (MQ=255)               aGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑Att                                                                                                                                     <  1:287368/151‑1 (MQ=255)               aGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGC‑GGGGGGGGGATT‑GTTtggggggtt                                                                                                                                      >  1:948677/1‑145 (MQ=255)                gTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGT‑GGGGGGGAGATT‑GTTTGGGGG‑Att                                                                                                                                     >  2:360851/1‑150 (MQ=255)                  ctctGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGGTTTTCGATAGGGGCTCGTGCG‑GGGGGGGTGTTTGGTTgggggggaa                                                                                                                                      >  1:991226/1‑143 (MQ=255)                    ctGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTaa                                                                                                                                   <  2:631676/148‑1 (MQ=255)                     tGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCTTGCT‑GGTGGGGAGTTT‑GTTGTGAACAATTAAACt                                                                                                                                >  2:347736/1‑151 (MQ=255)                     tGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGT‑GGGGGGGTGGTT‑GTTgggggggtttaaatt                                                                                                                                >  2:42811/1‑139 (MQ=255)                           tGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTtgatga                                                                                                                          <  1:975356/150‑1 (MQ=255)                           tGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTtgatg                                                                                                                           <  2:99496/149‑1 (MQ=255)                               ccAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGT‑TGGGGGGTGATT‑TTTGGGGGC‑ATTAAAATTGATGACa                                                                                                                        >  2:538594/1‑148 (MQ=255)                               ccAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGG‑GGGGGGGTGATT‑TTTTGGGGG‑GTTAAAAtttgtgtaaggg                                                                                                                     >  1:567467/1‑141 (MQ=255)                                cAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGCTAGTGGCTCGTGCT‑GGGGGGGTGATT‑GGTGGGGGG‑ATTAAACTTTATGACAGTg                                                                                                                     >  2:380980/1‑150 (MQ=255)                                      aTGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGCT‑GGGGGGGTGATT‑GTTTGGGGC‑ATTTAAATTTATGACAGTG‑AAAt                                                                                                                >  2:620756/1‑148 (MQ=255)                                           tctcTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGGGGGGTGGTT‑GTTGGGGGG‑ATTTAACTTGATGACAGTG‑GAATTGCCAtt                                                                                                         >  2:64744/1‑150 (MQ=255)                                           tctcTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCAtt                                                                                                         <  1:425437/150‑1 (MQ=255)                                           tctcTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCAt                                                                                                          <  2:592928/149‑1 (MQ=255)                                                      cagacagGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGCT‑GGGGGGGGGGTT‑GTTTGGGGG‑ATTTAAATTTGTGACCGTG‑AAAATTGCATTggggggggg                                                                                                >  1:211048/1‑141 (MQ=255)                                                             gCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCt                                                                                     <  2:13804/151‑1 (MQ=255)                                                                  aGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGGGGGGTGATT‑TTTTGGGGG‑ATTTAAATTTATGACAGTG‑GAAATGTCATTGGGGG‑GGGGGCGTTTAACtt                                                                                    >  1:728949/1‑147 (MQ=255)                                                                   gTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGT‑GGGGGGGAGATT‑TTTTGGGGG‑ATTTAAATTTTTGGAAGTG‑GAATTGCCCTTTGGGG‑GGGGCCGTTTAACtt                                                                                    >  1:112524/1‑146 (MQ=255)                                                                    ttCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGCTGGGGGGGAGAATT‑GTGGGGGGG‑ATTAACTTTGTGAACAG‑G‑GAATTGTCATTTGGGAGGGGGCGGTTAACCtcctcg                                                                                >  1:649101/1‑145 (MQ=255)                                                                      cGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGtt                                                                             <  2:971080/150‑1 (MQ=255)                                                                         ttACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGAt                                                                          <  2:80230/150‑1 (MQ=255)                                                                            cGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGT‑GGGGGGGAGGTT‑GTTTGGGGG‑ATTAAAATTTATGACAGGG‑GAATTTCCCTTTGGGA‑GGGGGCGGTTACCCTTATCGTTTATGc                                                                        >  2:939903/1‑149 (MQ=255)                                                                                aaaGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGT‑GGGGGGGTGATT‑TTTGGGGGC‑ATTAAAATTGGTTACAGTGAAAATTGCC‑TTGGGGG‑GGGGGCGGTAACCCTCATCGtttgtggag                                                                      >  2:637750/1‑140 (MQ=255)                                                                                 aaGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGT‑GGGGGGGTGATT‑GTTTGGGGG‑ATTAAAATTTATGACAGTG‑AAATTGCCATTGGTGA‑GGGGCCGTTAAACTTCATTGTTGATGCAGATc                                                                   >  2:575380/1‑149 (MQ=255)                                                                                 aaGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCaa                                                                 <  2:803756/151‑1 (MQ=255)                                                                                  aGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGGC‑GGGGGGGTGATT‑GTTTGGGGG‑ATTTAAATTTGTGAAAGGG‑AAAATGCCAATTGTGG‑GGGGGCGTTAACCTTTATCGTTTTTGGAGAACaa                                                                 >  1:486712/1‑150 (MQ=255)                                                                                    cGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGGGGGGTGGTT‑GGTGGGGGC‑ATTAAACTTTGTGACAGTG‑AAAATGTCCTTGGGGA‑GGGGGCGTTTAACTTCATCGTTTATGCAGATCaa                                                                 >  2:396078/1‑148 (MQ=255)                                                                                    cGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATgg                                                              <  1:794671/151‑1 (MQ=255)                                                                                     gAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGc                                                             <  2:500065/151‑1 (MQ=255)                                                                                            gaTTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGCG‑GGGGGGAAGATT‑TTTTGGGGC‑ATTAAAATTGTTGAAAGGG‑AAAATGCCATTTGGGG‑GGGGCCGTTTAACTTCATCCTTGGTGGAGAACAATGGGTGttta                                                       >  1:278529/1‑148 (MQ=255)                                                                                                   caggcaAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGGGGGGTGGTT‑GTTGGGGGC‑ATTAAAATTTATGACAGGG‑GAATTGCCATTTGTGA‑GGGGCCGGTAAACTTCATCGTTGATGCAGATCAATGGCTGTTTCAggg                                                   >  2:600961/1‑147 (MQ=255)                                                                                                    aggcaAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGGT‑GGGGGGGTGATT‑TTTGGGGGG‑ATTAAAATTTGTGACAGGG‑AAAATTCCATTGGGGG‑GGGGCCGTTAAACTTCCTTGTTGATGCAGATCAAAGGCTGTTTCAggg                                                   >  2:502876/1‑146 (MQ=255)                                                                                                          aaTCCATCGGCAGGTTTGTCGTTAGTGGCTCGGGCT‑GGGGGGGGGATT‑GTTGGGGGC‑ATTAAACTTGATGGCAGTG‑AAATTGCCATTGGGGG‑GGGGGCGGTAAACTTCATTGTTGATGCAGATCAAAGGCTGTTTAAGGGACAGGcttctt                                        >  2:601290/1‑151 (MQ=255)                                                                                                                  ggCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGtgtg                                <  1:378346/151‑1 (MQ=255)                                                                                                                    cAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGGTGGTT‑GTTGGGGGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGGGG‑GGGGCCGTTTACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGGAAAGcttcttttcgtgtggg                              >  1:833836/1‑141 (MQ=255)                                                                                                                     aGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGa                             <  2:560391/151‑1 (MQ=255)                                                                                                                                   tGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCt               >  2:104392/1‑151 (MQ=255)                                                                                                                                   tGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCt               >  1:147838/1‑151 (MQ=255)                                                                                                                                        cGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGAtt           <  2:164846/150‑1 (MQ=255)                                                                                                                                        cGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGAtt           <  2:1111/150‑1 (MQ=255)                                                                                                                                             t‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTc     >  1:828707/1‑151 (MQ=255)                                                                                                                                               ggAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTcc    <  2:967250/151‑1 (MQ=255)                                                                                                                                                gAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTccc   >  1:314379/1‑151 (MQ=255)                                                                                                                                                 aGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCCCt  >  1:854810/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                       GAAGATGGTGAGGAAGTCTCTGGCCTTGGGCCAGCCTATGCTTCTCTGGAAAACAGACAGGCAACAGTTCGATTACGTAAAAGCGAAGTGAGATTTGGCAGGCAAAATCCATCGGCAGGTTTGTCGTTAGTGGCTCGTGCT‑GGAGGGATGATT‑GTTGGGAGC‑ATTAAACTTGATGACAGTG‑AAATTGCCATTGGTGA‑GGTGCCGTTAACCTTCATCGTTGATGCAGATCAATGGCTGTTACAGGGACAGGCTTCTTGCAGTGTGCGAAGCAGCGATGTTCTGATTGTGCTCCCT  >  NC_000913/4573353‑4573646

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑