Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,622,802	0	A	T	40.6%	46.3 / 13.2	32	intergenic (+61/+158)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
Reads supporting (aligned to +/- strand):  ref base A (17/2);  new base T (0/13);  total (17/15)
Fisher's exact test for biased strand distribution p-value = 3.02e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAATATGAATGTTTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAAT  >  NC_000913/1622653‑1622947                                                                                                                                                           |                                                                                                                                                     gTAATATGAATGTTTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GAt                                                                                                                                                     >  2:463502/1‑151 (MQ=255)     tatGAATGTTTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑C‑GAttttt                                                                                                                                                 >  1:398673/1‑151 (MQ=255)              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)                                                                                                                                                           |                                                                                                                                                     GTAATATGAATGTTTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCAC‑AAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGT‑TACAGTTGTGTACAAGGGGC‑C‑T‑GATTTTTAT‑GACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAAT  >  NC_000913/1622653‑1622947

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: ‑