Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,622,802	0	A	T	43.9%	55.1 / 14.2	41	intergenic (+61/+158)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
Reads supporting (aligned to +/- strand):  ref base A (20/3);  new base T (0/18);  total (20/21)
Fisher's exact test for biased strand distribution p-value = 7.52e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGA  >  NC_000913/1622665‑1622945                                                                                                                                              |                                                                                                                                                 tttttATGGGCGTATTGGGAATAATTTTATTTTCTGGTTTTTTGGTCG‑TGTATTTCAGCAACAAATGGGATGACTAAT‑GAACGGAGATAATACTTAACCTAACCGGCAACTTGTTACAG‑TTGTGTACAAGGGGTA‑TGATTTTTATGACgg                                                                                                                                      >  2:697605/1‑150 (MQ=255)  ttttATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGc                                                                                                                                     <  1:443699/150‑1 (MQ=255)     tATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGaa                                                                                                                                  >  1:486670/1‑150 (MQ=255)         gCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGaaaaaa                                                                                                                              >  1:809273/1‑150 (MQ=255)                 gggAATAATTTTATTTTCTGGTTTTCTGGCCG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCa                                                                                                                     <  2:439452/150‑1 (MQ=255)                         tttttttttGT‑GTTTTCCGGCCGTCTTATTACACCCAAAAAGGGGATGAAAAAA‑GAAGGGAAATATCCCCTCCCCAACCCCCCCCTTTGTTAAAT‑TTGTGAACAAGGGGCT‑TTTTTTTTATGACGGAAAAAAAAAA‑CCGCCAGTAAACcg                                                                                                             <  2:764156/150‑1 (MQ=255)                            tattttCTGGTTTTCTGGCCG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACcggcgg                                                                                                         >  2:367901/1‑151 (MQ=255)                               tttctggttttctggCCG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACcggcgg                                                                                                         >  1:442849/1‑148 (MQ=255)                                     tttttctggCCG‑TTTTTTCCACCAAAAAAGGGGATGA‑TAATGGAAGGGAAATACCCCCCCCCCAACCCGCCCCTTTTTTAAAT‑TTGTGTA‑AAGGGGCCTTTTTTTTTAGGGGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGc                                                                                                  <  1:655927/148‑1 (MQ=255)                                        ttctggCCG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTg                                                                                               >  1:422757/1‑149 (MQ=255)                                           gggcgg‑cGTATTGCACCCACAAATGGATTTAATAAA‑GAAGGGATAAAAACCCACACAAAGCCGGCCCTTTTTTACGG‑GTGTATAAAGGGGGCG‑TGATTTTTATTAAGGAAAAAAAAAC‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATgg                                                                                          <  2:544614/150‑1 (MQ=255)                                              ccG‑CTTTTTTCACCCAAAAAGGGGATGACAAAT‑AAACGGAAATAACCCCCCCCCTACCCGCCCCCTTTTTACTG‑TTGTGAACAGGGGGCT‑TTTTTTTTAGGACGAAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGAt                                                                                        <  1:558387/150‑1 (MQ=255)                                              ccG‑CTTTTTCCACCCAAAAAGGGAATGATTAAT‑GAACGGAAATACCCCCCCCCCAACCCGCCCCTTTGTTCCAG‑TTGTGAAAAGGGGGCT‑TTTTTTTTAGGACGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGAt                                                                                        <  1:415521/150‑1 (MQ=255)                                              ccG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGTCGGCGAAAACACA‑CCGCCAGTAAACCGGCGGCGAAAGCTTGCCTGGAt                                                                                        >  1:394489/1‑150 (MQ=255)                                               cggcttATTCCACCCAAAAAGGGGATGAAAAAT‑AAAGGGAAAT‑ACCCCCCCCCCAACCGCCCCCTTTTTACCGTTTGTGAAAAGGGGGCG‑TGTTTTTTATGAGGCCAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATgg                                                                                          <  2:822708/143‑1 (MQ=255)                                                g‑cgTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCCTgg                                                                                          >  2:795321/1‑146 (MQ=255)                                                   gTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGAtt                                                                                   >  1:806821/1‑151 (MQ=255)                                                              aaaaaGGGGATGAATAAT‑GACCGGAAAAAACCCCCCCCCGACCCGGCCCTTTGTTAAGG‑TTGTGTAAAGGGGGCT‑TTTTTTTTTGGAGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCt                                                                        <  1:577419/149‑1 (MQ=255)                                                                aaaTGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCttt                                                                      >  1:237863/1‑151 (MQ=255)                                                                    gggATGACTAAT‑GAAGGGAAATAACCCCTCCCCAACCCGCCCCTTTTTTACAG‑TTGTGAACAGGGGGCC‑TGTTTTTTATGGCGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCtttt                                                                     <  1:157876/148‑1 (MQ=255)                                                                       aTGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCt                                                                >  1:712087/1‑150 (MQ=255)                                                                        tGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTa                                                               >  1:125247/1‑150 (MQ=255)                                                                         gACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAAc                                                             >  1:646762/1‑151 (MQ=255)                                                                             aaT‑GAACGGAGATAATCCCTCACCTAACCGGCCACATGTTACAG‑TTGGGTACAAGGGGCC‑TGATTTTGATGACGGCGAAAAAAAA‑ACGCCAGTAAACCGGCGGTGAACGACTGCCTGGAACTAATTGTGTTTTGTTTGTAcaccaa                                                              >  2:339304/1‑141 (MQ=255)                                                                                     ggaaaaaaccccTCCCCAACCCGCCCCCTTGCTACGG‑TTGTGTACAGGGGGCT‑TGTTTTTTAGGCCGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCa                                                        <  1:752156/136‑1 (MQ=255)                                                                                       agaTAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGGTAGATTTGTGTTTTGCTTTTACGCTAAAAGGCATTTTCCt                                                 >  2:113353/1‑150 (MQ=255)                                                                                       agaTAACCCCCCACCTACCCGCCCCTTTTTTACTG‑TTGTTTACAAGGGGTT‑TGTTTTTTATGGCGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCt                                                 <  1:250267/150‑1 (MQ=255)                                                                                           aaTCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACt                                            >  1:737291/1‑151 (MQ=255)                                                                                               ccctcccctcccGGCCCCTTTTTAAGG‑TTTTTTAAAAGGGGCC‑TTTTTTTTAAGGCGGAAAAAAAAAACCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGAt                                         <  1:368018/141‑1 (MQ=255)                                                                                                         cgggCCCTTTGTTAAGT‑TTGTGAAAAGGGGGCT‑TGTTTTTTATGACGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGtt                              <  2:203069/149‑1 (MQ=255)                                                                                                          cGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTg                             >  2:634899/1‑151 (MQ=255)                                                                                                             ccttgtGTTACTG‑TTGGGAAAAAGGGGCT‑TTTTTTTTATGACGAAAAAAAAACT‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGaca                          <  2:672190/146‑1 (MQ=255)                                                                                                             ccctTTTTTACAT‑TTGTGAAAAGGGGGCT‑TTTTTTTTATGACGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTg                             <  1:733942/148‑1 (MQ=255)                                                                                                                    ttACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGc                   >  1:129552/1‑151 (MQ=255)                                                                                                                    ttACAG‑TTGTGAACAGGGGGCT‑TTTTTTTTATGACGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTa                     <  1:175376/149‑1 (MQ=255)                                                                                                                            ttgtgaaaaGGGGGC‑TTTTTTTTTTGAAGAAAAAAAAAAC‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAg              <  2:347529/142‑1 (MQ=255)                                                                                                                             gtgaaaagggggCG‑TGTTTTTTATAACGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGtt            <  2:340528/142‑1 (MQ=255)                                                                                                                                     ggggCT‑TGTTTTTTAGGAGGAAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtctc       <  1:740382/147‑1 (MQ=255)                                                                                                                                     ggggCCTTGTTTTTTAGGAGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGtt            <  1:600238/143‑1 (MQ=255)                                                                                                                                       ggCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatga  >  2:687215/1‑150 (MQ=255)                                                                                                                                       ggCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatga  >  1:10234/1‑150 (MQ=255)                                                                                                                                              |                                                                                                                                                 TTTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGA  >  NC_000913/1622665‑1622945

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑