Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,903,692	0	C	A	43.1%	87.3 / 40.0	58	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
Reads supporting (aligned to +/- strand):  ref base C (5/28);  new base A (25/0);  total (30/28)
Fisher's exact test for biased strand distribution p-value = 8.35e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01

ACAAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTAAC  >  NC_000913/2903548‑2903840                                                                                                                                                 |                                                                                                                                                       aCAAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCa                                                                                                                                                  <  2:673902/151‑1 (MQ=255)   aaGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAACACTCCtt                                                                                                                                                >  2:254474/1‑151 (MQ=255)          atTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑c                                                                                                                                         <  2:190230/150‑1 (MQ=255)           ttAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAGTTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTTAAAACACCCCTTAGCCT‑c                                                                                                                                         >  2:246030/1‑149 (MQ=255)            tAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑Caa                                                                                                                                       <  2:700234/150‑1 (MQ=255)             aaCTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑Caaa                                                                                                                                      <  2:781138/150‑1 (MQ=255)              aCTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTTAAAACAACCATTATCCT‑Caaaa                                                                                                                                     >  1:320584/1‑150 (MQ=255)                tACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACACTCATTAACCT‑Ccaaaaa                                                                                                                                   >  1:83935/1‑148 (MQ=255)                 acacTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACaaa                                                                                                                                 <  1:440340/151‑1 (MQ=255)                          gTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACACTCATTAGCCC‑CAAAAAAAAAACaaaa                                                                                                                          >  2:480634/1‑148 (MQ=255)                            cTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACACTCATTATCCT‑Caaaaaaaaaaaaaa                                                                                                                           >  1:160400/1‑146 (MQ=255)                                aGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAACACTCATTATACT‑CAAaacaaaaacaaa                                                                                                                           >  1:393519/1‑142 (MQ=255)                                     aaaaGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATttatt                                                                                                             <  2:551190/151‑1 (MQ=255)                                      aaaGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTAAAAACACTCATTTTCCT‑CAAAAAAAAAAAAAAAATCCAGATttatt                                                                                                             >  1:772084/1‑150 (MQ=255)                                      aaaGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATttatta                                                                                                            <  1:755818/151‑1 (MQ=255)                                       aaGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTGTAAAAACACTCATTAACCT‑CAAAAAAAAAACAAAAATCCAGAtttttt                                                                                                             >  2:287128/1‑149 (MQ=255)                                        aGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACACCCATTTACCT‑CCAAAAAAAAAAAAAATTTCAGATttatt                                                                                                             >  2:426124/1‑148 (MQ=255)                                            aaTACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAAc                                                                                                      <  2:307120/151‑1 (MQ=255)                                             aTACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTTAAAAAAACTCATTATCCT‑CAAAACAAAAACAAAAATTCAGATTTTTTACtt                                                                                                         >  1:530512/1‑147 (MQ=255)                                               aCGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCa                                                                                                    <  2:797368/150‑1 (MQ=255)                                                  aaTCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGa                                                                                                <  1:182544/151‑1 (MQ=255)                                                               cAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTa                                                                                    <  2:611446/150‑1 (MQ=255)                                                                  ttttCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTGTAAAAACCCCCATTAACCT‑CAAAAAAAAAAAAAAAATCCCGATTTATTACTTAAACAAAGAATAAAAAACTTaaaa                                                                                 >  2:1014874/1‑150 (MQ=255)                                                                          tAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAAAACTCATTATCCT‑CAAAAAAAAAACAAAAATCCAGATTTATTTATTTACCAAAGAAAAAAAAACTTaaaaaa                                                                               >  1:488586/1‑144 (MQ=255)                                                                            aaGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACACTCATTTACCT‑CAAAAAAAAAACAAAATTTCCGATTTTTTAATTAAACAAATAATAAAAAACTTAAAAAAaataatttt                                                                      >  1:309618/1‑146 (MQ=255)                                                                                aTGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTc                                                                 <  2:792270/151‑1 (MQ=255)                                                                                    aCTGCATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTaaa                                                             <  2:332241/151‑1 (MQ=255)                                                                                       ggATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGa                                                           <  2:871959/150‑1 (MQ=255)                                                                                          tatCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAAAACTCATTAACCT‑CCAAAAAAAAAAAAAATTCCAGATTTTTTATTTTAACAATGAAAAAAAAACTTAAAAAAAATAATT‑TTTTTTTTAaaaaaa                                                        >  1:13455/1‑150 (MQ=255)                                                                                              tttATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACACTCATTAACCT‑CAAAAAAAAAAAAAAAATCCCGATTTATTAATTTAACAAAAAATAAAAAAATTAAAAAAAAAAATT‑TTATTTTTAaaaaaaaa                                                      >  1:840936/1‑148 (MQ=255)                                                                                               ttATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAAtt                                                    <  2:660641/149‑1 (MQ=255)                                                                                                 aTTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACACTCATTAACCT‑CAAAAAAAAAAAAAAAATCCAGATTTATTAATTTAACAAAGAAAAAAAAAATTAAAAAAAAAACTT‑TTATTTTAAAAAAAAAAATaa                                                  >  1:487517/1‑149 (MQ=255)                                                                                                  ttCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAACACTCATTAGCCT‑CAAAAAAAAAACAAAATTTCAGAATTATTAATTAAACAAAGAAAAAAAAACTTAAAAAAAATAATG‑TTTTTTTTAAAAAAAAAATaaaa                                                >  2:630162/1‑148 (MQ=255)                                                                                                  ttCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATTTAAAAAAACACATTATCCC‑CAAAAAAAAAACAAAAATCCACATTTTTTTTTTAAAAAAAAAAAAAAAAACATAAAAAAAAAAAAT‑TTATTTTAAAAAAAAAAATaaaa                                                >  2:405629/1‑148 (MQ=255)                                                                                                    cATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAgg                                              <  2:746042/150‑1 (MQ=255)                                                                                                    cATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGc                                             <  2:787856/151‑1 (MQ=255)                                                                                                         gAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTaa                                        <  2:200416/151‑1 (MQ=255)                                                                                                          aaCTATTCATCAACAGCGTATAGAGGCGGTTTTGTAAAAACAACCATTAGGCC‑CAAAAAAAAAAAAAAACTCCAAATTTTTTAATTTAACAAAAAAAAAAAAACATAAAAAAAATAATT‑TTTTTTTTAAAAAAAAAATAAAAAGCATTaa                                        >  2:306975/1‑150 (MQ=255)                                                                                                          aaCTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAAACACTCATTAACCT‑CAAAAAAAAAACAAACTTTCCGATTTATTTCTTAAACAAAAAATAAAAAACTTTAAAAAAATAATG‑TTTTTTTTAAAAAAAAAATAAAAAGCATTaa                                        >  2:1014962/1‑150 (MQ=255)                                                                                                               ttCATCAACAGCGTATAGAGGCGGGTATTTAAAAACACCCATTAGCCC‑CAAAAAAAAAACAAAAATTCAGATTTATTTCTTTAACAAATAAAAAAAAACTTAAAAAAAAAAATGTTTTTTTTAAAAAAAAAATAAAAAGGAATAAAttaa                                    >  2:365721/1‑148 (MQ=255)                                                                                                                 catcaACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAatat                                <  1:604089/151‑1 (MQ=255)                                                                                                                 catcaACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAata                                 <  2:258503/150‑1 (MQ=255)                                                                                                                    caACAGCGTATAGAGGCGGTTATGTAAAAACACTCCTTTACCTCCAAAAAAAAAAAAAAATTCC‑CATTTTTTACTTTAACAAAGAATAAAAAACTTTAAAAAAATAATT‑TTTTTTTTAAAAAAAAAATAAAAAGGATTAATTTAATAtt                               >  2:679721/1‑149 (MQ=255)                                                                                                                     aaCAGCGTATAGAGGCGGTTTTTTTAAAAACCTCCTTTGCCT‑CAAAACAAAAACAAACATTCAGAATTTTTACTTTAACAAAGAAAAAAAAAATTAAAAAAAATAATG‑TTATTTTTAAAAAAAAAATAAAAAGCAATAATTTAAAAATaa                             >  1:425887/1‑150 (MQ=255)                                                                                                                     aaCAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTaaa                            <  2:1010343/151‑1 (MQ=255)                                                                                                                        aGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTaaaaaa                         <  1:186870/151‑1 (MQ=255)                                                                                                                          cGTATAGAGGCGGTTATGTAAAAACAAACATTTACCT‑CCAAACAAAAAAAAAAATCCAGATTTATTACTTAAACCAAGAAAAAAAAACTTTAAAAAAATACTG‑TTTTTTTAAAAAAAAAAATAAAAAGCAATAATTTAAAATTaaaaaaa                        >  2:365364/1‑150 (MQ=255)                                                                                                                                  ggCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGAtt               >  2:588815/1‑151 (MQ=255)                                                                                                                                    cGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTa              >  1:860131/1‑150 (MQ=255)                                                                                                                                      gTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTaaaa           <  1:540638/151‑1 (MQ=255)                                                                                                                                        tATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAAtt         >  2:371785/1‑151 (MQ=255)                                                                                                                                        tATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAAt          <  1:265489/150‑1 (MQ=255)                                                                                                                                         aTGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAAttt        <  1:224168/151‑1 (MQ=255)                                                                                                                                            tAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCtt     >  1:83274/1‑151 (MQ=255)                                                                                                                                             aaaaCCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCtt     <  1:858655/150‑1 (MQ=255)                                                                                                                                             aaaaCCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCtt     >  1:856550/1‑150 (MQ=255)                                                                                                                                             aaaaCCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTa    <  2:30685/151‑1 (MQ=255)                                                                                                                                               aaCCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTAAc  <  2:1006142/151‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                       ACAAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTATGTAAAACCACTCATTAGCCT‑CAAAACAAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAACAAGCTTAAAAAATATACTG‑TTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTAAC  >  NC_000913/2903548‑2903840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑