Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,903,692	0	C	A	41.7%	55.5 / 32.2	48	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
Reads supporting (aligned to +/- strand):  ref base C (5/23);  new base A (20/0);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 3.28e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01

TTTACAAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTAACGA  >  NC_000913/2903545‑2903842                                                                                                                                                      |                                                                                                                                                           tttACAAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCa                                                                                                                                                          <  1:234144/150‑1 (MQ=255)      aaGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCAtt                                                                                                                                                    <  1:92638/151‑1 (MQ=255)         gAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑c                                                                                                                                                <  1:557669/151‑1 (MQ=255)           atatTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCt                                                                                                                                              <  1:422660/151‑1 (MQ=255)             atTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TTAAAACAATCCtt                                                                                                                                                    >  2:88458/1‑144 (MQ=255)                aaCTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTT‑TTAAAACAAACATTTG‑CCC‑Caaa                                                                                                                                         >  2:267456/1‑150 (MQ=255)                   tACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTT‑TAAAAACACTCATTAG‑CCT‑Caaaaaa                                                                                                                                      >  1:378458/1‑148 (MQ=255)                               cTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTG‑TAAAAACACTCCTTAG‑CCC‑CCAAAC‑Aaaaaaaaaaat                                                                                                                          >  1:73732/1‑146 (MQ=255)                                 ttAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTc                                                                                                                         <  1:357709/148‑1 (MQ=255)                                  tAGAATAAAAGACAATACTAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAg                                                                                                                      <  1:574111/150‑1 (MQ=255)                                  tAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTT‑TAAAAACACTCCTTTT‑TCC‑CAAAAC‑AAAAACAAAATTcc                                                                                                                        >  1:359722/1‑148 (MQ=255)                                     aaTAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATT‑TAAAACCACTCATTTA‑CCT‑CCAAAA‑AAAAAAAAAACTCCCGAttt                                                                                                                  >  1:602518/1‑151 (MQ=255)                                               aaTACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTT‑TTAAAACAACCATTAA‑CCTCCAAAAA‑AAAAAAAAAATTCCAATTtttttatt                                                                                                            >  1:659087/1‑146 (MQ=255)                                               aaTACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTG‑TTAAACCAATCATTAG‑CCT‑CAAAAA‑AAAAAAAAACATCCAGAtttttttattta                                                                                                         >  1:585611/1‑144 (MQ=255)                                                  aCGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCaa                                                                                                     <  1:323394/151‑1 (MQ=255)                                                  aCGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCa                                                                                                      <  2:388530/150‑1 (MQ=255)                                                   cGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTT‑TTAAAACAATCAATAT‑CCT‑CAAAAA‑AAAAAAAAAAATCCAGAAttttttttt                                                                                                           >  2:458908/1‑140 (MQ=255)                                                        cGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATa                                                                                               <  1:645882/151‑1 (MQ=255)                                                              ttATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAg                                                                                         <  2:471830/150‑1 (MQ=255)                                                              ttATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAg                                                                                         <  2:471787/150‑1 (MQ=255)                                                                   aaTTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTT‑TTAAAAAACTCATTTA‑ACT‑CCAAAA‑AAAAAAAAAATTCCCGATTTTTTTTTTAAACAAATAATAaa‑aaacatta                                                                                    >  2:666610/1‑144 (MQ=255)                                                                         cACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAatat                                                                             <  2:659052/151‑1 (MQ=255)                                                                           cTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGGTTTTTT‑TAAAAAAAACCCTTAA‑CCT‑AAAAAA‑AAAAAAAAAATTCCGAATTTTTTATTTAA‑CAATAAAAAAA‑AAACTTaaaaaaaa                                                                              >  2:609386/1‑146 (MQ=255)                                                                                 gTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTT‑TAAAAAAACACATTAA‑ACC‑CAAAAC‑AAAAAAAAAAATTCCGAATTATTATTTTAACAAAAAAAAAA‑AAAATTAAAAAAAATAATGTTAt                                                                     >  1:333989/1‑151 (MQ=255)                                                                                 gTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTAt                                                                     <  2:154150/151‑1 (MQ=255)                                                                                          ggATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTG‑TAAAAACCCTCATTAA‑CCT‑CAAAAA‑AAAAAAAAAATTCCAGATTTATTAATTAAACAAAGAAAAAA‑AAACTTAAAAAAAATAATGTTAtttttaaaa                                                             >  1:583262/1‑143 (MQ=255)                                                                                          ggATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAg                                                              <  1:642126/149‑1 (MQ=255)                                                                                          ggATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGaa                                                            <  2:50693/151‑1 (MQ=255)                                                                                                cTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTA‑TAAAACCACTCATTTA‑CCT‑CAAAAA‑AAAAAAAAACTTTCAGAATTATTTATTAACCAAATAACAAA‑AAGACTAAAAAATATTCTTCTTTTTTTAAAAAAAAAtt                                                      >  1:684460/1‑151 (MQ=255)                                                                                                 tttATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTGTTAAAAAAACCCTTTGC‑CCC‑CAAAAA‑AAAAAAAAAATTCCAG‑TTTTTTTCTTTACCAAAAAAAAAA‑AAAATTAAAAAAAAAAATGTTATTTTTAATaaaaaa                                                        >  2:2633/1‑148 (MQ=255)                                                                                                      tCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATT‑TAAAAACACTCCTTAA‑CCC‑CAAAAA‑AAAAAAAAAAATTCCGAATTATTTATTAAACAATAAAAAAC‑AAAATTAAAAAAAATAATGTTTTTTTTAaaaaaaaaaaaaaa                                                  >  1:471945/1‑143 (MQ=255)                                                                                                       cATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTT‑TAAAAAAACTCCTTAG‑CCT‑CCAAAA‑AAAAACAAAAATTCAGATTTTTTAATTAAACAAAGAATAAA‑AAAAATAAAAAAAATAATGTTATTTTAAAAAAAAAAATaaaa                                                  >  1:13494/1‑146 (MQ=255)                                                                                                       cATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATT‑TAAAAACACCCCTTTT‑CCT‑CAAAAA‑AAAAACAAAAATTCCGATTTTTTTTTTTAACCATGAAAAAA‑AAACTTAAAAAAAATAATTTTTTTTTTAAAAAAAAAATaa                                                    >  1:689758/1‑146 (MQ=255)                                                                                                           aGAACTATTCATCAACAGCGTATAGAGGCGG‑ATATT‑TAAAAACACCCATTAGACCC‑CCAACA‑AAAAAAAAACTCCCCATTTTTTTATTTAACCAAGAAAAAAA‑AAAATTAAAAAA‑ATACTTTTTTTTTAAAAAAAAAAATaaaaagc                                               >  1:670689/1‑142 (MQ=255)                                                                                                            gAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTT‑TAAAAACACACATTAT‑CCC‑CAAAAA‑AAAAAAAAAAATCCCGATTTTTTTTTTTAACAAAGAAAAAA‑AAACTTAAAAAAAAAAAATTTTTTTTaaaaaaaaaaaaaaaaagca                                              >  1:742589/1‑137 (MQ=255)                                                                                                            gAACTATTCATCAACAGCGTATAGAGGCGG‑TTTTG‑TTAAAACACCCCTTAT‑TGT‑CCAAACAAAAAACAAAATT‑CAGGCTTGTTATTTAACCAAAGGATAACAAAGATTAAAAAA‑ATAATTTTATTTTTAACAAAAAATTTAAAggaacta                                           >  1:252625/1‑145 (MQ=255)                                                                                                             aaCTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAAt                                         <  2:280795/151‑1 (MQ=255)                                                                                                                     atcaACAGCGTATAGAGGCGG‑TTATG‑TGAAAACACCCCTTAG‑ACT‑CAAAAC‑AAAAAAAAAAATTCAAATTTATTAATTAAACAAAAAAAAAA‑AAACCTAAAAAAAAAAATGTTTTTTTTTAAAAAAAAATAAAAAACAATAATTTAata                                   >  2:311102/1‑149 (MQ=255)                                                                                                                         aCAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTaaaa                             <  1:706860/151‑1 (MQ=255)                                                                                                                           aGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTaaaaaa                           <  1:31793/151‑1 (MQ=255)                                                                                                                           aGCGTATAGAGGCGG‑TTATG‑TAAAAACACCCACTTG‑ACT‑CAAAAC‑AAAAACAAACTTCCAGATTTTTTACTTAACCAATGAAAAAC‑AAACTTTAAAAATATAATTTTATTTTTAAAAAAAAAATAAAAAGCAATTATTATATATTaaaaa                            >  1:165605/1‑150 (MQ=255)                                                                                                                             cGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTaaaaaaa                          <  2:47277/150‑1 (MQ=255)                                                                                                                                      gCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCATATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTa                <  2:583618/151‑1 (MQ=255)                                                                                                                                         g‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTaaa              >  1:26580/1‑150 (MQ=255)                                                                                                                                           ttATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTaaaa             <  1:26570/150‑1 (MQ=255)                                                                                                                                            tATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAAt            <  2:201316/150‑1 (MQ=255)                                                                                                                                                   aaaCCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAACTTAAAAAATATACTATTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTaa     <  2:586293/151‑1 (MQ=255)                                                                                                                                                     aCCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTAACg   >  1:465707/1‑151 (MQ=255)                                                                                                                                                      ccACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTAACg   >  2:172263/1‑150 (MQ=255)                                                                                                                                                      ccACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTAACGa  <  1:235603/151‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                           TTTACAAGGAATATTAACTACACTCGATGTCTTTAGAATAAAAGACAATACGAATCGCACTTTATCAATTTTCACTTAAAGTATGAACTGGATATCTTTATTCATAAGAACTATTCATCAACAGCGTATAGAGGCGG‑TTATG‑TAAAACCACTCATTAG‑CCT‑CAAAAC‑AAAGACAAACTTCCAGATTTATTACTTAACCAATGAATAAC‑AAGCTTAAAAAATATACTGTTATTCTAAAGAAAAAATTAACAGGCATTAATTCAATATTAAAAAAATAATAGATTAAAATTTCTTAACGA  >  NC_000913/2903545‑2903842

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑