Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,947,850	0	C	T	42.2%	57.4 / 20.8	45	E40K (GAA→AAA)	hdfR	flhDC operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (6/20);  new base T (19/0);  total (25/20)
Fisher's exact test for biased strand distribution p-value = 7.46e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGT  >  NC_000913/3947704‑3947991                                                                                                                                                   |                                                                                                                                              aTGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCAGTTGATTTTTCAGt                                                                                                                                           >  2:49528/1‑151 (MQ=255)   gTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGtt                                                                                                                                          <  1:33241/150‑1 (MQ=255)           gTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTc                                                                                                                                 <  1:703637/151‑1 (MQ=255)             aTGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGGTCACACCCAGGTGGTTTTTCAGTTTTCTGATTCg                                                                                                                                >  2:567836/1‑150 (MQ=255)               gcgcCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGTTCACACCCCGTTGGTTTTCCCGTTTTCTTGTTCGaa                                                                                                                              >  1:445581/1‑150 (MQ=255)                 gcCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGGAAAGGTTCACACCCAGGTGATTTTTTTGTTGTCTGATTCGaaa                                                                                                                             >  2:402259/1‑149 (MQ=255)                 gcCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGATGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGc                                                                                                                           >  2:573790/1‑151 (MQ=255)                   cACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTTACACCCAGGTGATTTTTCAGTTGTCTGATTTGAAAGCTc                                                                                                                         >  1:581317/1‑151 (MQ=255)                           tACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCActgctg                                                                                                                  <  1:535281/150‑1 (MQ=255)                           tACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCACACCCAGTTGATTTTTCAGTTTTCTGATTTGAAAGCTCa                                                                                                                        >  2:287118/1‑144 (MQ=255)                                gcggcCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTggg                                                                                                            <  1:287146/151‑1 (MQ=255)                                    ccTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAg                                                                                                        <  1:526282/151‑1 (MQ=255)                                    ccTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAg                                                                                                        <  1:357733/151‑1 (MQ=255)                                    ccTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAg                                                                                                        <  1:152848/151‑1 (MQ=255)                                      tGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGATCACACCCCGGTGATTTTTCAGTTTTCTGATTTGAAAAATCACTGCTGACTggg                                                                                                            >  2:616284/1‑145 (MQ=255)                                         cAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTCACACCCCGTTTATTTTTCAGTTGTCTGATTCGAAAGCTCCCTGCTGACTGGGTTAg                                                                                                        >  1:319589/1‑146 (MQ=255)                                            gTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGGTCACACCCCAGTGATTTTTCAGTTTTCTGGTTTGAAAGATCACTGCTGACTGGGTCAGATAGGGCg                                                                                                >  2:172733/1‑151 (MQ=255)                                               cTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGCGGAAAGGGTTACACCCCGTTTGTTTTTCAGTTTTCTGAATTGGAAGCACACTCCCGACTGGGTGAGATCGAGAGAt                                                                                              >  1:668386/1‑150 (MQ=255)                                                        gTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGCGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGCAAGCTCACTGCTGCCTGGGTCAGATAGAGCGATTCAGCCGCTc                                                                                    <  1:466325/151‑1 (MQ=255)                                                          ttCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCCGTTGATTTTTCAGTTGTTTGATTCGGAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTTAGCCGCTCg                                                                                   >  1:113361/1‑150 (MQ=255)                                                              gCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCa                                                                               <  2:658295/150‑1 (MQ=255)                                                              gCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGCGGAAAGGGTCACAACCAATTTTTTTTTCCGTTTTTTTTTTACAAAAATCCATGCTGACAGGGTCAGGAAGAGGGATTcttccccctgcc                                                                                 >  1:558323/1‑137 (MQ=255)                                                               cATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCAGGTGGTTTTTCAGTTTTCTGATTCGAAAACTCACTGCTGACTGGGTCAGATAGAGGGATTTAGCCCCCCGACCaa                                                                              >  2:673334/1‑150 (MQ=255)                                                                  aaGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGt                                                                           <  2:159400/150‑1 (MQ=255)                                                                   aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGTTTACCCCCACTTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGGCAGATAAAGCGAATTAGCCCCCCGACCCAAATg                                                                          >  1:658711/1‑150 (MQ=255)                                                                          agtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGtt                                                                   <  2:89795/150‑1 (MQ=255)                                                                                 cACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCAGTTGATTTTTTAGTTGTCTGGTTCGAAAACTCACTGCTGGCTGGGGCAGATAGAGAGATTTAGCCGCCCGACCCAAAAGACGCGGTCCGCTaa                                                            >  2:578841/1‑150 (MQ=255)                                                                                  aCCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCCGTTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAATGACGCGGTCGGCTaa                                                            >  1:637622/1‑149 (MQ=255)                                                                                   ccGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACtt                                                         <  2:451154/151‑1 (MQ=255)                                                                                      gCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCa                                                      <  1:632536/151‑1 (MQ=255)                                                                                       cAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAAGGTCACACCCCGTTGATTTTTCAGTTGTCTGATTCGAAAGATCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCCAAATGACGCGTTCGGCTAACtt                                                         >  2:275503/1‑147 (MQ=255)                                                                                        aGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCACACCCCGTTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGGCAGATAGAGCGATTCAGCCGCTCGACCAAAGGGACGCGGTCGGCCAACTTCCAgg                                                    >  1:630086/1‑151 (MQ=255)                                                                                              tAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCACACCCCGGTGATTTTTCAGTTGTTTGATTTGAAAACTCACTGCTGACTGGGGCAGATAGAGCGATTTAGCCGCTCGACCAAAATGACGCGTTCGGCTAACTTCCAGGAAAGtt                                              >  1:452942/1‑151 (MQ=255)                                                                                               aaaCGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGttt                                             <  2:88514/151‑1 (MQ=255)                                                                                                  cGGATATTGTTTCTGTGGCGGGGGAAAAAGTTCACACCCCGGTGATTTTTCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGGCAGATAGAGCGATTCAGCCGCTCGACCAAAATGACGCGTTCGGCTAACTTCCCGGAAAGgtttt                                           >  2:354703/1‑150 (MQ=255)                                                                                                            ttCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCg                                 <  2:583974/150‑1 (MQ=255)                                                                                                            ttCTGTGGCGGGGGAAAAAGTTCACAACCAGTTGATTTTCCATTTTTCTGATTCGAAAAATCACTGCTGGCTGGGGCAGATAGAGGGATTTAGCCGCCCGACCAAAGTGAAGCGTTTGGCTAACTTCCAGGAAAGTTTTTAACAATTc                                   >  2:458923/1‑148 (MQ=255)                                                                                                                    cGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCcac                          >  2:567748/1‑149 (MQ=255)                                                                                                                     gggTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCTATTCAGCCGCTCGACCAAAGTGACGCGTTCTGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGt                       <  2:587105/151‑1 (MQ=255)                                                                                                                         gAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGct                    <  2:136700/150‑1 (MQ=255)                                                                                                                            aaGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTcc                <  2:664290/151‑1 (MQ=255)                                                                                                                            aaGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTcc                <  2:34863/151‑1 (MQ=255)                                                                                                                                    cacCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAatt        >  2:139870/1‑151 (MQ=255)                                                                                                                                        cAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTAttt    <  2:332023/151‑1 (MQ=255)                                                                                                                                          gTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGt  >  2:354677/1‑151 (MQ=255)                                                                                                                                                   |                                                                                                                                              ATGTCGTGAGGTATGCGCCACCTCCTTACGGGCGGCCTGCCAGGTGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGGCTAACTTCCAGGAAAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGT  >  NC_000913/3947704‑3947991

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑