Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,622,815	0	C	A	41.7%	61.6 / 23.5	48	intergenic (+74/+145)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
Reads supporting (aligned to +/- strand):  ref base C (25/3);  new base A (0/20);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.06e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAA  >  NC_000913/1622666‑1622963                                                                                                                                                          |                                                                                                                                                      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)                                                                                                                                     gggccttgttttttAGGACGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatg                     <  1:673634/142‑1 (MQ=255)                                                                                                                                      ggCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatga                    >  1:10234/1‑150 (MQ=255)                                                                                                                                      ggCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatga                    >  2:687215/1‑150 (MQ=255)                                                                                                                                           tttttttttGGACGGCAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGt                <  2:486522/147‑1 (MQ=255)                                                                                                                                             ttttttAGGAGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGtt               <  1:635093/148‑1 (MQ=255)                                                                                                                                              tttttATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTaa             >  2:390213/1‑150 (MQ=255)                                                                                                                                                 ttATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACgg         >  2:224358/1‑151 (MQ=255)                                                                                                                                                  tATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACgg         >  1:616623/1‑150 (MQ=255)                                                                                                                                                   aTGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGATTTTTCCTGCAATGATAACGAAACGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTCAACg          >  2:238811/1‑148 (MQ=255)                                                                                                                                                    tGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAAATTTGTGTTTTGATTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAg       >  2:847286/1‑150 (MQ=255)                                                                                                                                                         gCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGCATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTaa  >  2:402747/1‑150 (MQ=255)                                                                                                                                                          |                                                                                                                                                      TTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCG‑CGTATTTCAGCCACAAATGGGATGACTAAT‑GAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAG‑TTGTGTACAAGGGGCC‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAA  >  NC_000913/1622666‑1622963

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑