Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,622,816	0	G	A	51.6%	3.6 / 45.5	31	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
Reads supporting (aligned to +/- strand):  ref base G (14/1);  new base A (0/16);  total (14/17)
Fisher's exact test for biased strand distribution p-value = 5.66e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.48e-05

TTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGC  >  NC_000913/1622666‑1622959                                                                                                                                                              |                                                                                                                                                 ttttATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑Cg                                                                                                                                                  >  2:263432/1‑151 (MQ=255)  tttATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑Cg                                                                                                                                                  >  2:397319/1‑150 (MQ=255)                gggAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGcc                                                                                                                                    <  2:589289/149‑1 (MQ=255)                     taatTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAAc                                                                                                                             >  2:292290/1‑151 (MQ=255)                        ttttttttttGGTTTTTCGGGCCGC‑TTTTTCAACCCCAAAATGGGTTGAATAAGGAAGGAAAAAAACCCCTC‑CCAAACCCGCCCCTTTTATAAATTGGTGAAC‑AGGGCC‑C‑TGGATTTTTAT‑TACGG‑CAAAAAAAAA‑CCGCCAGTAAACcg                                                                                                                           <  1:404381/150‑1 (MQ=255)                             ttttctggttttctggCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGt                                                                                                                      >  1:276957/1‑150 (MQ=255)                               ttctggttttctggCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGt                                                                                                                      >  1:279271/1‑148 (MQ=255)                               ttctggttttctggCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGa                                                                                                                    >  2:327650/1‑150 (MQ=255)                                    tttttcgggCCGCGTTTTTCACCCAA‑AAAGGGGATGAATAATAAAGGGAAAAACCCCCTCCCCAACCCGCCCCTTTGT‑TACGTTTGTGAAAAGGGGGC‑T‑T‑TTTTTTTAG‑GGGGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATg                                                                                                                 <  2:573147/147‑1 (MQ=255)                                         ctggCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTATAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATg                                                                                                         >  2:459816/1‑151 (MQ=255)                                          tggCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATgg                                                                                                        >  2:293199/1‑151 (MQ=255)                                                tgTATTCCACCCAA‑AAAGGGAATAATTAATGAAGGAAAATATTCCCCCCCCTACCCGCCCCTTTGT‑TTTATTTGTGTACGA‑GGGC‑C‑T‑TTTTTTAAA‑TGGGG‑CAAAAAAAAAGCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATa                                                                                                     <  2:590612/147‑1 (MQ=255)                                                    ttccacccAA‑AAAGGGAATGACAAATAAAGGGAAAAACCCCCTCCCCAACCCGCCCCTTTGT‑TACGTTTGTTTA‑AAGGGGCTT‑T‑TTTTTTTAG‑GGCGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCa                                                                                                           <  2:170812/132‑1 (MQ=255)                                                       cAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGtt                                                                                           >  2:162548/1‑151 (MQ=255)                                                             c‑aAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCtt                                                                                     >  1:28035/1‑151 (MQ=255)                                                               aaagggaatcataaaTGATGGGAGATATTCCCCCACCAACCCGGCCTTTTGT‑TAGGTTTGTGAACAGGGGGC‑T‑T‑TTTTTTAAT‑GAAGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGtt                                                                                           <  2:561741/131‑1 (MQ=255)                                                               aaaGGGGATAACAAATGAAGGGAAATAACCCCTCCCCAACCCGCCCCTTTTT‑TACATTTGTGAACAGGGGGC‑T‑T‑TTTTTTTAG‑GACGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGtt                                                                                           <  2:498001/144‑1 (MQ=255)                                                                                    gagaTAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTcc                                                                >  1:577717/1‑150 (MQ=255)                                                                                       aTAACCCCCCCCCAACCCGCCCCTTTGT‑TACGGTTTTGTA‑AAGGGGC‑CTT‑GTTTTTTAG‑GAGGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCAt                                                                     <  2:388949/142‑1 (MQ=255)                                                                                                         ggCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGtt                                            >  1:107166/1‑149 (MQ=255)                                                                                                           ccctTTTT‑TACTTTTGTGTA‑AAGGGGC‑C‑T‑TTTTTTTGTGGAGGG‑AAAAAAAAAT‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGtt                                            <  1:376442/147‑1 (MQ=255)                                                                                                              ttttt‑tACTGTTTTGTA‑AAGGGGC‑C‑T‑TTTTTTTTA‑GGCGGAAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGaca                                        <  2:2966/144‑1 (MQ=255)                                                                                                                 gT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGt                                    >  1:400042/1‑149 (MQ=255)                                                                                                                        gTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATc                              >  1:632947/1‑149 (MQ=255)                                                                                                                         tggtgaACAAGGGGC‑T‑T‑TTTTTTTAG‑GACGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCAt                               <  1:463255/145‑1 (MQ=255)                                                                                                                             gtaaagggggC‑T‑T‑GTTTTTTTT‑GACGA‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGtt                          <  1:459168/142‑1 (MQ=255)                                                                                                                              aacggggggC‑G‑T‑GTTTTTTAG‑GCGGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGCGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtc                       <  2:519815/145‑1 (MQ=255)                                                                                                                              aaCAGGGGGC‑T‑T‑GTTTTTTAG‑GGCGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtct                      <  2:675/150‑1 (MQ=255)                                                                                                                               aCAGGGGGC‑C‑T‑TTTTTTTAT‑GACGG‑CAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCACGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATCTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtct                      <  2:58228/150‑1 (MQ=255)                                                                                                                                      gC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatgaat              >  2:282210/1‑151 (MQ=255)                                                                                                                                            ttttttttAT‑GACGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatgaat              <  2:160292/145‑1 (MQ=255)                                                                                                                                               tttttAT‑GAGGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTa          <  2:305352/149‑1 (MQ=255)                                                                                                                                                     t‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGc  >  2:430789/1‑151 (MQ=255)                                                                                                                                                              |                                                                                                                                                 TTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGC  >  NC_000913/1622666‑1622959

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑