Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	42.5%	50.4 / 28.3	48	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (3/24);  new base T (20/0);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.81e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGA  >  NC_000913/4604195‑4604491                                                                                                                                                      |                                                                                                                                                     aCTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttct                                                                                                                                                     <  2:571605/151‑1 (MQ=255)   tCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAtttttttttt                                                                                                                                                   >  2:922778/1‑151 (MQ=255)        gAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAtttttttttttttt                                                                                                                                               >  2:274070/1‑148 (MQ=255)        gAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAtttttttttttt                                                                                                                                                 >  2:6304/1‑148 (MQ=255)          aaaaTGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGcc                                                                                                                                            >  1:950706/1‑151 (MQ=255)               gCGTCATGAGTAGTATCTGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATga                                                                                                                                        <  1:1050327/150‑1 (MQ=255)               gCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTtttttcttttttttccc                                                                                                                                           >  1:284068/1‑141 (MQ=255)                   cATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCTTTTTTTTTTTTTTTGCCATGAGAAg                                                                                                                                    >  1:198622/1‑150 (MQ=255)                   cATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAg                                                                                                                                    <  2:478053/150‑1 (MQ=255)                   cATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGt                                                                                                                                   <  1:267681/151‑1 (MQ=255)                     tGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCtttttttttttttttccgcgggaagt                                                                                                                                   >  2:64687/1‑135 (MQ=255)                     tGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAggg                                                                                                                                  >  1:914727/1‑148 (MQ=255)                       agtagtATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAg                                                                                                                                    >  2:190996/1‑146 (MQ=255)                       agtagtATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgc                                                                                                                               <  1:871729/151‑1 (MQ=255)                             aTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCag                                                                                                                           >  1:80197/1‑149 (MQ=255)                                ggTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAgg                                                                                                                      <  1:720562/151‑1 (MQ=255)                                 gTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCCGGGAggg                                                                                                                     >  1:286124/1‑151 (MQ=255)                                 gTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAggg                                                                                                                     <  2:522899/151‑1 (MQ=255)                                 gTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAggg                                                                                                                     <  2:203841/151‑1 (MQ=255)                                      gagaGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTa                                                                                                                 <  2:245687/150‑1 (MQ=255)                                       agagATTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGAAACTTTTTGTTTTTTTGGCACGGGAAGTGGGGGTAGAGAgggct                                                                                                                   >  2:198797/1‑145 (MQ=255)                                         agTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGGGAAGTGAGGGCAGAGAGGGAttttttt                                                                                                             >  2:913764/1‑146 (MQ=255)                                             tATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGGGCAGGGAGGGATTATCTTTcc                                                                                                          >  1:725063/1‑150 (MQ=255)                                                 cAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCc‑tgacg                                                                                                    <  2:933730/151‑2 (MQ=255)                                                            cGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTTCCTGGGAAGGGAGCGCAGGGGGGGGTTATTTTTCC‑TGACCGAAATGGCg                                                                                           >  2:547046/1‑149 (MQ=255)                                                              ggTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTa                                                                                       <  2:1091096/151‑1 (MQ=255)                                                                tAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCCTTAGAAGTGAGGGCAGGGGGGGGTTATTTTTCCTTGAC‑GAACTGGCGAttta                                                                                      >  2:814974/1‑148 (MQ=255)                                                                 aaCCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAg                                                                                     <  1:532913/150‑1 (MQ=255)                                                                    ccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTc                                                                                 <  1:437038/151‑1 (MQ=255)                                                                       tataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTCCCTGGGAAGGGAGGGCGGAGAGGGATTATTTTGCC‑TGGCTGAAATTGGGGTTTAGttttc                                                                                >  1:606077/1‑147 (MQ=255)                                                                       tataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCcg                                                                               <  2:384808/150‑1 (MQ=255)                                                                        ataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGGGAAGTGAGCGCAGAGAGGGGTTATTTTTCC‑TGACTGAACTGGCGGTTAAGTTTcc                                                                                >  1:736737/1‑148 (MQ=255)                                                                           aGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGACATTTTTTTTTTTTTTTCCATGAGAAGTGAGGGGCGGGAGGGATTTTCTTTTT‑TTAGTGAACCGGGGATTAAAATTCCGCGGAc                                                                          >  2:360266/1‑151 (MQ=255)                                                                              tCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTTCCTGGAAAGGGGGGGCAGGGAGGGGTTATATTTGC‑TGTGTGAAATGGGGATTAAATTTTCCCGTAccc                                                                        >  1:624543/1‑150 (MQ=255)                                                                              tCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGACATTTTTTTTTTTTTTTCCCTTAGGAGTGAGCGCAGAGAGGGGTTTTTTTTCC‑TTGCTGTACCGGCGGTTTAGTTTCcccgctgc                                                                         >  2:671429/1‑145 (MQ=255)                                                                                       ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTa                                                                <  2:418417/149‑1 (MQ=255)                                                                                           cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCCTGGGAAGGGAGCGCAGAGGGGGATTTTCTTGCC‑TGACTGGACTGGGGATTAAGGTTTCGCGTAccccggggtttggtatt                                                          >  1:124545/1‑137 (MQ=255)                                                                                            aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTg                                                         <  1:344457/151‑1 (MQ=255)                                                                                                  gAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGgatg                                                   <  1:395662/151‑1 (MQ=255)                                                                                                    gTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGgatga                                                  <  2:383119/150‑1 (MQ=255)                                                                                                       aTTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTCTGTCTTGAGGAGTGAGCGCCGAGAGGGGTTTTTTTTCC‑TGACTTGACTGGCGGTTAAGGTTCCGCCGACCCGGCGGTTAGTTATTGCGggtgat                                                 >  1:198533/1‑148 (MQ=255)                                                                                                       aTTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGgatgatgat                                              <  2:862939/151‑1 (MQ=255)                                                                                                          tCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGatat                                            <  2:37689/150‑1 (MQ=255)                                                                                                            aGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTGCACGAGAAGAGAGAGCCGCAGGGGGTTTTTTTTCC‑TGCCTCAACTGGCGAATAAGGTTTCCCGCAACCCGGGTTTAGTTTTTTCGgatgatg                                                >  2:1148541/1‑144 (MQ=255)                                                                                                            aGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGa                                         <  1:413574/151‑1 (MQ=255)                                                                                                                 gCCATGTCGCGGATCTCGTTTGCGGCGGTCTTTTTTTCTTTTTTTGCCATGAGAAGGGTGCGGAGAGAGGGGGTATCTTGCC‑TTACTGAACTGGGGGTTAAGTTTCCGCGTAACCGGCGTTTTGTTATTTCGGGTGGTGATATTTaaagtc                                    >  1:1126504/1‑147 (MQ=255)                                                                                                                      gTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTg                               <  1:1015535/151‑1 (MQ=255)                                                                                                                        cgcgGATCTCGTTTGCGGCGGTTATTTTTTTTTTTTTTGCCATGAGAAATGAGCGGAGAGAGGGGTTATTTTTCC‑TGGCTTGACTGGGGCGTAAATTTCCGCGGACCCGGCGGTTAGATGTTGGGGGTGATGAttttttagagcgg                                  >  2:1069142/1‑137 (MQ=255)                                                                                                                                 cGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGGGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTc                       <  1:181562/148‑1 (MQ=255)                                                                                                                                   tttGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGGGCGGAGGGGGAGTATTTTGTC‑TGTCTTAACTGGCGATTAAGTTTCCGCGCACCCGGCGTTTTGGTTTTGGGGGTGATGGTATTTAAGCTCGGGCGATTGGTTCGtt                    >  2:323924/1‑149 (MQ=255)                                                                                                                                    ttGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGt                  <  2:67553/150‑1 (MQ=255)                                                                                                                                         gcggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCAt            >  1:1065889/1‑151 (MQ=255)                                                                                                                                         gcggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCAt            <  1:671456/151‑1 (MQ=255)                                                                                                                                                ttttttCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCt     >  2:92175/1‑151 (MQ=255)                                                                                                                                                    ttctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGa  >  2:803438/1‑150 (MQ=255)                                                                                                                                                    ttctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGa  >  2:234469/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                     ACTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCC‑TGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGA  >  NC_000913/4604195‑4604491

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑