Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,571,384	0	T	A	38.5%	88.2 / 13.2	52	Y64F (TAT→TTT)	yjiR	putative DNA‑binding transcriptional regulator/putative aminotransferase
Reads supporting (aligned to +/- strand):  ref base T (11/21);  new base A (20/0);  total (31/21)
Fisher's exact test for biased strand distribution p-value = 8.91e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTTTGCTTAACGGAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGCAATTTCTCCCCGTGACGATACAGCCCTTGCTC  >  NC_000913/4571240‑4571529                                                                                                                                                    |                                                                                                                                                  cTTTTGCTTAACGGAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑GT‑GGGGTTTTCGGTGTGGGGCAAAAAAAacc                                                                                                                                              >  1:813139/1‑150 (MQ=255)   tttGCTTAACGGAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGa                                                                                                                                            <  2:57978/150‑1 (MQ=255)      gCTTAACGGAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑GT‑GGGGTTTCCGGTTTGGGGCAAAAAAAcac                                                                                                                                              >  2:194670/1‑143 (MQ=255)      gCTTAACGGAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAAcgc                                                                                                                                        <  1:829914/151‑1 (MQ=255)         tAACGGAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CC‑GGGGTTTTCGTTGTGCGACCAAAAAAACCCAACGCgg                                                                                                                                      >  1:411612/1‑150 (MQ=255)         tAACGGAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACCCGG‑GG‑CTGGGGCTTTTC‑TTGTTTGCCAAAATAAaccccaagcg                                                                                                                                       >  1:655623/1‑142 (MQ=255)          aaCGGAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CC‑GGGCTTTTCGGTTTGCGACAAAAAAACCCCaaaacgg                                                                                                                                      >  1:1096401/1‑144 (MQ=255)           aCGGAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTg                                                                                                                                   <  2:424001/151‑1 (MQ=255)              gAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGGGTTACGTTGTGGGGCAAAAAAAACCCAACGCCGCTGCgg                                                                                                                                >  1:303953/1‑151 (MQ=255)              gAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGGACTGGG‑GG‑GG‑GGGGTTTTCGGTGGGGGGCAAAAAAAACCggaaacggcgggg                                                                                                                                 >  1:743160/1‑138 (MQ=255)               aaCAATGGAACTGTCGCTATGCGCCTCCAGCATAGCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATACCCCGACCGCGGATGCGGa                                                                                                                               <  2:702041/151‑1 (MQ=255)                         cTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GGCCT‑GGGGTTT‑CGGTTTGGGGCAAAAAAAACCCAAcgccggcgccggggg                                                                                                                            >  2:306718/1‑132 (MQ=255)                            tCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑GT‑GGGGTTTTCGTTTTGGGGCAAAAAAAACCCCACGCGGCCGCGGGGGGGTGAGGtt                                                                                                                    >  1:1039662/1‑149 (MQ=255)                              gCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATc                                                                                                                <  2:454919/151‑1 (MQ=255)                               cTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGCGGG‑CG‑GGGCTTT‑CGGTGTGCGACAAAAAAAACCCCACGCGGCCGCGGGGGGATGAGCtt                                                                                                                    >  1:44576/1‑146 (MQ=255)                                tATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGG‑GG‑GTGGGGCTTTACGTT‑TGCGGCAAAAAAAACCCAACGCGGGCGCGGGGGGATGAGCTTCATCGt                                                                                                              >  1:634111/1‑151 (MQ=255)                                  tGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGGTTTTAGGTGGGCGGCAAAAAAAACCCCAAGCGGccggtgggggatgag                                                                                                                       >  2:774234/1‑126 (MQ=255)                                    cgcCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTcc                                                                                                          <  1:44320/151‑1 (MQ=255)                                       cTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGGCTTTCGTTGTGCGGCAAAATAACCCCAACGCGGCTGGGGGGGGATGAGCTTCATCGTCTcc                                                                                                          >  1:650277/1‑148 (MQ=255)                                        tCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAg                                                                                                        <  2:713878/149‑1 (MQ=255)                                             cATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGa                                                                                                 <  2:655408/151‑1 (MQ=255)                                                atCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGGTTTTCGTTGTGCGGCCAAAAAAACCGCACGCGGCCGCGGGGGGAGGAGCTTCCTCCTCCCCcgcggccggt                                                                                                >  2:208779/1‑143 (MQ=255)                                                atCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATa                                                                                               <  2:62701/150‑1 (MQ=255)                                                    aGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CC‑GGGGGTTTCGTTGTGCGACAAAAAAAACCCAAAGCCGGCGCGGGGGGGTGAGCTTTATCCTCTCCCGCGTCttgtaagcc                                                                                           >  2:735747/1‑142 (MQ=255)                                                     gCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGGGTTACGGTGTGGGGCAAAAAAACCCCAACGCGGGTGGGGGGGGGTGAGGTTTCTCGGCTCCAGCGGCCGGTACGcc                                                                                           >  1:173040/1‑149 (MQ=255)                                                       aCCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CC‑GGGGTTTTCGTTGTGCGACAAAAAAAACCCAACGCGGCTGCGGGGGGATGAGCTTTATCCTCTCCAGCGTCTTGTACGcc                                                                                           >  1:494893/1‑147 (MQ=255)                                                        ccTGATCCCACTGGGTAATTTCCGCCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCctgctg                                                                                      <  2:584212/151‑1 (MQ=255)                                                            aTCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGGGTTACGCTGTGGGACAAAAAAACCCGCAAGCGGGCGCGGGGGGGTGTGGTTCCTCGTCTCCAACGTCTGGAAAGCCCGCTGCAc                                                                                   >  2:22472/1‑150 (MQ=255)                                                              cccACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CC‑GGGCTTTTCGGTGTGCGACAAAAAAACCCCAAAGCGGCCGCGGGGGGATGAGGCTCATCGTCTCCAGCGGCTGATACGCCCGCTTCACgg                                                                                 >  1:960923/1‑150 (MQ=255)                                                                      gTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTTCGTTTTGCGGCAAAAAAAACCCAACGCGGCTGCGGAGGGATGAGCTTCATCGTCTCCAGCGGCTGATACGCCCGCTGCACgg                                                                                 >  1:396123/1‑142 (MQ=255)                                                                        aaTTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATaat                                                                       <  1:591982/150‑3 (MQ=255)                                                                         aTTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTAATGGC‑GG‑CC‑GGGGTTTTCGGTGTGGGGCAAAAAAAACCCAACGCGGCTGCGGGGGGGTGAGCTTTATCGTCTCCCGCGGCTGATAAGCCCGCTGCCCgg                                                                                 >  1:771931/1‑139 (MQ=255)                                                                           ttCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGAc                                                                    <  1:566495/150‑1 (MQ=255)                                                                               aCCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑GT‑GGGGTTTTCGGTGTGCGGCAAAATAACCCGAACGCGGCCGCGGGGGGATGAGCTTCATCGTCTCCCGCGTCTGATACGCCTGCCGCACGGGGGTGATACTGACGcc                                                                 >  1:387309/1‑149 (MQ=255)                                                                                        tGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑GT‑GGGGTTTTCGGTGTGGGGCAAAAAAAACCCAACGCGGCCGGGGGGGGATGAGGTTTATAGTCTCCAGCGGCTGATACGCCTGCTGCACGGGGCTGGTAATGAAGCCGGGCTCCTGAc                                                      >  1:679461/1‑151 (MQ=255)                                                                                             cGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCGGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTaa                                                  <  2:751916/150‑1 (MQ=255)                                                                                                  gcgTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTgcg                                            <  1:52354/151‑1 (MQ=255)                                                                                                           gcggTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACgg                                   >  1:89257/1‑151 (MQ=255)                                                                                                           gcggTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACgg                                   <  2:969604/151‑1 (MQ=255)                                                                                                            cggTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACgg                                   >  2:885102/1‑150 (MQ=255)                                                                                                             ggTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGc                                  >  2:223599/1‑150 (MQ=255)                                                                                                                   ggc‑gg‑cT‑GGGTTTTTCGTTGCGCGACAAAATAACCCGAACGCGGCTGCGGAGTTTTGAGCTTTATCGTCTCCAGCGTCTGTTACGCCTGCTGCACGGTGCTTATACTGTCTCCGTGCTCCTGCCTTAAGCTGCGCACCGACGTCAtttt                             <  2:742925/149‑1 (MQ=255)                                                                                                                       gg‑cT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGCAATTTCTccc                        <  2:107448/151‑1 (MQ=255)                                                                                                                             gggCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGCAATTTCTCCCCg                      <  2:360610/149‑1 (MQ=255)                                                                                                                               gCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGCAATTTCTCCCCGTGAc                  <  1:437715/151‑1 (MQ=255)                                                                                                                               gCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGCAATTTCTCCCCGTGAc                  <  1:160170/151‑1 (MQ=255)                                                                                                                                  ttACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGCAATTTCTCCCCGTGACGAt               >  2:842026/1‑151 (MQ=255)                                                                                                                                    aCGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGCAATTTCTCCCCGTGACGATa              <  1:1050462/150‑1 (MQ=255)                                                                                                                                    aCGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGCAATTTCTCCCCGTGACGATAc             >  2:52350/1‑151 (MQ=255)                                                                                                                                       ttGTGCGACAAACTAACCCGTAAGCGGCTGCGGAGTTATGAGCTTCTTCGTCTCCAGCGAATGATACGCCTGCTGCACGTTGCTGATACTGACGCCGTGCTCCTGACTTACGCTGCGCACCGACGGCAATTTCTCCCCGTGCCGCTACAGc          >  2:672967/1‑151 (MQ=255)                                                                                                                                            cGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGCAATTTCTCCCCGTGACGATACAGCCCTTg     >  1:72621/1‑151 (MQ=255)                                                                                                                                               cAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGCAATTTCTCCCCGTGACGATACAGCCCTTGCTc  >  1:677365/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                                  CTTTTGCTTAACGGAACAATGGAACTGTCGCTATGCGCCTCCAGCATATCCAGCACCTGATCCCACTGGGTAATTTCCACCGGGCGCTGCACCGGACGCGTCATCGGCGGTACTGGC‑GG‑CT‑GGGCTTTACGTTGTGCGACAAAATAACCCGAACGCGGCTGCGGAGTGATGAGCTTCATCGTCTCCAGCGTCTGATACGCCTGCTGCACGGTGCTGATACTGACGCCGTGCTCCTGACTTAAGCTGCGCACCGACGGCAATTTCTCCCCGTGACGATACAGCCCTTGCTC  >  NC_000913/4571240‑4571529

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: ‑