Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,903,692	0	C	A	57.5%	27.6 / 59.7	40	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
Reads supporting (aligned to +/- strand):  ref base C (2/15);  new base A (23/0);  total (25/15)
Fisher's exact test for biased strand distribution p-value = 3.38e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.45e-07

TTTTTACAAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTT  >  NC_000913/2903543‑2903834                                                                                                                                                      |                                                                                                                                                   tttttACAAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAcc                                                                                                                                                   <  1:119148/151‑1 (MQ=255) tttttACAAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAc                                                                                                                                                    <  2:467146/150‑1 (MQ=255) tttttACAAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAc                                                                                                                                                    <  1:156208/150‑1 (MQ=255)           gAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCGCTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTGTAAAAACAC‑TCATTat                                                                                                                                         >  1:352989/1‑149 (MQ=255)           gAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTTAAAACAC‑TCacttt                                                                                                                                         >  2:627632/1‑146 (MQ=255)           gAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACAC‑TCATTAg                                                                                                                                         >  1:303599/1‑150 (MQ=255)             atatTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTGTTAAAAAAC‑TCATTaac                                                                                                                                        >  2:83904/1‑147 (MQ=255)                   aCTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAAc                                                                                                                               <  2:121318/151‑1 (MQ=255)                                 cTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTTAAACCAC‑CCCCTTTCCT‑CAAAACaaaaaacaacctc                                                                                                                  >  2:526844/1‑140 (MQ=255)                                 cTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTTAAAACAA‑TCAATATCCT‑CAAAAAAAAAAA‑AAACATc                                                                                                                 >  2:543038/1‑150 (MQ=255)                                 cTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACAA‑ACATTTTCCT‑CAAAACAAAAAA‑AAACttt                                                                                                                 >  2:525834/1‑149 (MQ=255)                                 cTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAAAAC‑TCATTAACCT‑CAAAAAAAAAAA‑AAAATTc                                                                                                                 >  1:281039/1‑150 (MQ=255)                                       aaTAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGAttt                                                                                                          <  1:610383/151‑1 (MQ=255)                                       aaTAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGAt                                                                                                            <  1:272516/149‑1 (MQ=255)                                       aaTAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGAt                                                                                                            <  1:374595/149‑1 (MQ=255)                                        aTAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAACAC‑TCATTAACCT‑CAAAACAAAAAC‑AAAATTCCCGAtttt                                                                                                         >  1:470556/1‑150 (MQ=255)                                                            cACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTTAAAACACACCATTA‑CCC‑CAAAAAAAAAACAAAAATTCCA‑ATTTATT‑AATTAAACAAAGAATaaa                                                                                    >  2:329170/1‑150 (MQ=255)                                                            cACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAAc                                                                                    <  1:29367/151‑1 (MQ=255)                                                              cTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTAAAAAAAC‑ACATTTTCCT‑CAAAACAAAAAA‑AAAATTCCAGATTTATT‑ACTTAACCAATGAATAaaaa                                                                                  >  2:462095/1‑151 (MQ=255)                                                                 tATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCt                                                                               <  2:80638/151‑1 (MQ=255)                                                                           cACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACAA‑TCATTTGCCT‑CAAAACAAAAAA‑AAACTTCCAGATTTTTT‑TATTAACCAAAGAAAAACAAACTTAAAAAaaat                                                                     >  2:426587/1‑151 (MQ=255)                                                                                aaaGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGt                                                                <  2:175292/151‑1 (MQ=255)                                                                                 aaGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTGTAAAAACAC‑TCATTAACCTCCAAAAAAAAAAA‑AAACTT‑CAGATTTTTT‑TATTAAACAAAGAAAAAAAAACTTAAAAAAAATAATGtt                                                               >  1:3182/1‑151 (MQ=255)                                                                                   gTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAACAC‑TCATTTACCT‑CAAAACAAAAAC‑AAACTTTCAGATTTATT‑TATTAACCAATGAATAAAAAACTTAAAAAAAATACTGTTAt                                                             >  1:340690/1‑151 (MQ=255)                                                                                     aTGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGTTATTc                                                           <  2:45454/151‑1 (MQ=255)                                                                                       gAACTGGATATCTTTATTCATAAGAACTATCCATCAACAGCGTATAGAGGCGGTTTTTTTAAAACAC‑TCATTTTACT‑CAAAACAAAAAC‑AAAATTTCAGATTTTTT‑TATTAAACAAATAATAAAAAAAATAAAAAATATACTGTttttttt                                                         >  2:434504/1‑148 (MQ=255)                                                                                            ggATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTGTAAAAACAC‑TCATTAGCCT‑CAAAACAAAAAA‑AAAATTCCCGATTTTTT‑ACTTAAACAATGAATAAAAAACTTAAAAAAAATAATGTTATTCTTAaaaa                                                    >  1:84297/1‑151 (MQ=255)                                                                                            ggATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTGTAAAAACAC‑TCATTAGCCT‑CAAAAAAAAAAC‑AAAATTTCAGATTTTTT‑ACTTAACCAATGAAAAAAAAACTTAAAAAATATAATGTTATTTTaaaaaa                                                    >  1:33965/1‑151 (MQ=255)                                                                                                 tCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAACAC‑TCATTAACCT‑CAAAAAAAAAAA‑AAACTTTCAGATTTATT‑ATTTTAACAAAAAAAAACAAACTTAAAAAAAATAATTTTTTTTTTAaaaaaaaaa                                               >  1:331421/1‑150 (MQ=255)                                                                                                         cATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTGTAAAAACAC‑CCATTAACCT‑CAAAAAAAAAAC‑AAAAATCCAGATTTTTTAATTTAACCAA‑GAATAACAAACTTAAAAAAAATAATGTTTTTTTTAAAAAAAAAATaaaaaga                                       >  2:287681/1‑146 (MQ=255)                                                                                                         cATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAACAC‑TCCTTAACCT‑CCAAAAAAAAAA‑AAAATTCCAGATTTATT‑TCTTTACCAATGAATAACAAACTTAAAAAAAAAAATTTTATTTTTAAAAAAAAAATaaaaag                                        >  1:305067/1‑146 (MQ=255)                                                                                                              gAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACAA‑ACATTTTCCC‑CAAAACAAAAAA‑AAAAATTCCGATTTATT‑ACTTTAACAAATAAAAAAAAACTTAAAAAAAATAATTTTATTTTAAAAAAAAAAATAAAAAGCAttta                                  >  2:239538/1‑149 (MQ=255)                                                                                                               aaCTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCAATAGGCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAAt                                 <  1:420979/151‑1 (MQ=255)                                                                                                                 cTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTc                               <  1:159796/151‑1 (MQ=255)                                                                                                                 cTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTc                               <  2:84296/151‑1 (MQ=255)                                                                                                                   aTTCATCAACAGCGTATAGAGGCGGTTATGTAAAAACAC‑TCATTAGCCT‑CCAAAAAAAAAC‑AAACTTCCAGATTTTTT‑ACTTTAACAAAGAATAACAAACTTAAAAAAAATACTGTTATTTTAAAGAAAAAAATAAAAGGCATTAATTCaa                             >  1:55574/1‑151 (MQ=255)                                                                                                                      catcaACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAatat                          <  2:225516/151‑1 (MQ=255)                                                                                                                      catcaACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAatat                          <  2:470546/151‑1 (MQ=255)                                                                                                                      catcaACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAatat                          <  1:321589/151‑1 (MQ=255)                                                                                                                      catcaACAGCGTATAGAGGCGGTTATGTAAAAACAC‑CCATTAGCCT‑CAAAAAAAAAAA‑AAACTTCCAGATTTTTT‑ATTTAAACAAAGAATAAAAAGCTTTAAAAATATACTGTTATTTTAAAAAAAAAATTAAAAGGCATTAATTCAatat                          >  1:151449/1‑151 (MQ=255)                                                                                                                                gTATAGAGGCGGTTATGTAAAAACAC‑TCCTTTGCCT‑CCAAACAAAAAA‑AAACTTCCCGATTTTTT‑AATTTAACAATAAATAAAAAAATTAAAAAAAAAACTGTTTTTTTTAAAAAAAAAATAAAAAGCATTAATTTAAAATTAAAAAaata                >  2:538994/1‑151 (MQ=255)                                                                                                                                      agGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAg            <  1:593776/149‑1 (MQ=255)                                                                                                                                              aTGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAAttt  >  2:589080/1‑151 (MQ=255)                                                                                                                                                      |                                                                                                                                                   TTTTTACAAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCAC‑TCATTAGCCT‑CAAAACAAAGAC‑AAACTTCCAGATTTATT‑ACTTAACCAATGAATAACAAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTT  >  NC_000913/2903543‑2903834

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑