Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,622,816	0	G	A	39.0%	44.8 / 24.5	41	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
Reads supporting (aligned to +/- strand):  ref base G (23/2);  new base A (0/16);  total (23/18)
Fisher's exact test for biased strand distribution p-value = 1.48e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAAACT  >  NC_000913/1622666‑1622966                                                                                                                                                            |                                                                                                                                                        ttttATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCg                                                                                                                                                         >  1:595798/1‑151 (MQ=255)  tttATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCg                                                                                                                                                         >  1:250852/1‑150 (MQ=255)     aTGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGaaa                                                                                                                                                      <  2:667453/150‑1 (MQ=255)      tGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGaaaa                                                                                                                                                     >  1:229054/1‑150 (MQ=255)                              tttctggttttctggCCGCGTATTTCAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTg                                                                                                                            >  2:631983/1‑150 (MQ=255)                               ttctggttttctggCCGCGTATTTCAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTg                                                                                                                            >  1:227310/1‑149 (MQ=255)                                     ttttctggCCGCGTATTTCAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTg                                                                                                                    >  1:497510/1‑151 (MQ=255)                                                 gTATTTCAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCT‑ATTGTT‑AGAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGACTGCTTGCATGGATAGAtt                                                                                                        >  2:699689/1‑151 (MQ=255)                                                  ttttacAGCCAAAAATGGT‑ATGATAAATAAAGGGAAATACCCCCCCCCTTCCCCGCCCC‑CTTTTT‑AGGGTTTTGAACAAGGGCC‑T‑TGTTTTTTTGGAGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAg                                                                                                           <  2:638324/142‑1 (MQ=255)                                                  tATTTCAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGAttt                                                                                                       >  1:664113/1‑151 (MQ=255)                                                    ttccacccAAAAAGGGA‑ATGATTAATGAAGGGAAATAACCCCCCCCCAACCCGGCCC‑TTTGTT‑ACATTTGTGAAAAGGGGGC‑T‑TGTTTTTGAGGAGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGAttt                                                                                                       <  1:641218/143‑1 (MQ=255)                                                       cAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGtt                                                                                                  >  1:39515/1‑151 (MQ=255)                                                          cccaaaaTGGGAATGATTAATAACCGGAGATAACCCCCCCCCAACCCGCCCC‑TTTGTT‑ACAGTTTGGCAAAAGGGCC‑C‑TTTTTTTTATAACGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTtgtg                                                                                                    <  1:304415/143‑1 (MQ=255)                                                          ccACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTg                                                                                               >  2:501918/1‑151 (MQ=255)                                                          ccAAAAAGGGG‑ATAATAATTGAAGGGAAATAA‑CCCCCCCCCAACCCGCCC‑CTTTTTAAAATTTGTTTACGGGGGGC‑T‑TTTTTTTTAGGAGGGAAAAAAAATA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGtttt                                                                                                <  2:671829/150‑1 (MQ=255)                                                            aaaaaTGGA‑ATGATAAATGAAGGGAAATACCCCCTCCCCAACCCGCCCC‑TTTTTT‑ACATTTGTGAACAAGGGGC‑C‑TGTTTTTTATGACGAAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTtgtg                                                                                                    <  2:414676/142‑1 (MQ=255)                                                             caAATGGG‑ATGACTAATGAACGGAGCTAATCACTCCCCTAACCGCCCC‑CTTGTT‑ACAGTTGTGTACAAGGCGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAACCCGGCGGTGAATGCTTGCATGGCTAGATTTCTGTTTTTCtt                                                                                            >  2:36114/1‑151 (MQ=255)                                                              aaaTGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCttt                                                                                           >  1:662160/1‑151 (MQ=255)                                                              aaaTGGG‑ATCAATAATGAAGGGAAATAACCCCCCCCCTACCCGCCCC‑TTTTTT‑ACAGTTGGAAACAGGGGCC‑T‑TTTTTTTTATGAGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGttt                                                                                                 <  1:174361/145‑1 (MQ=255)                                                               aaTGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCtttt                                                                                          >  2:444771/1‑151 (MQ=255)                                                                 tGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTAc                                                                                        >  2:117409/1‑151 (MQ=255)                                                                          cTAATGAACGGAAATAACCCCCCACCTACCCGGCCC‑TTTTTT‑ACATTTGTTAACAAGGGGC‑T‑TGTTTTTTATGAGGAAAAAAAAAAT‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACa                                                                                 <  2:310553/150‑1 (MQ=255)                                                                           tAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAgg                                                                               >  2:333368/1‑151 (MQ=255)                                                                             aggAACGTATATCATCCC‑CCCCAAACCCGCCCTCTTATT‑ATAGTTGTTTACAGGGGTC‑C‑TGTTTTTAAAGCCGAAGAAAAAAAC‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAg                                                                                <  2:284935/146‑1 (MQ=255)                                                                             aTGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGc                                                                              >  2:432449/1‑150 (MQ=255)                                                                                       atatTCCCACACCCACCCGGCCC‑CTTTTT‑AATTGTGTGTACAGGGGCC‑C‑TTTTTTTCAGGACGCCAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCa                                                                   <  1:623932/151‑1 (MQ=255)                                                                                       aTAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGc                                                                    >  1:418828/1‑150 (MQ=255)                                                                                            ccccccccaacccGCCCC‑TTTGTA‑CCATTTGTG‑AAAAGGGGC‑CTTTTTTTTTATGCCGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACt                                                                 <  1:592615/137‑1 (MQ=255)                                                                                            cccTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGAt                                                              >  2:483721/1‑151 (MQ=255)                                                                                                       ccccccc‑cTTTTT‑ACAGTTGTGAACAAGGGTC‑T‑TTTTTTTTATGAGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAAt                                                       <  2:663879/143‑1 (MQ=255)                                                                                                                  gTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGt                                           >  2:670606/1‑149 (MQ=255)                                                                                                                         ggtttgtACAAGGGGCTT‑TTTTTTTTATG‑CGGCAAAAAAAAAGCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGc                                        <  2:595173/143‑1 (MQ=255)                                                                                                                          ttGTGAAAAGGGGGC‑T‑TGTTTTTTATGCGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCa                                    <  1:391872/149‑1 (MQ=255)                                                                                                                           ttgtgaCAAGGGGC‑CTTTTTTTTTAGGCGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCa                                    <  1:547752/144‑1 (MQ=255)                                                                                                                                  aaGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGAGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCa                           >  1:649480/1‑150 (MQ=255)                                                                                                                                      ggggtcttttttttATGACGGCAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatg                        <  1:395194/142‑1 (MQ=255)                                                                                                                                        c‑c‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatgaat                     >  2:161779/1‑150 (MQ=255)                                                                                                                                          c‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATACTTGCATGGATAGATTTGTGTTTTGCTTTTACGCCAACAGGCATTTTCCTGCACTGGTAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGt                   >  2:121050/1‑151 (MQ=255)                                                                                                                                               tttttATGAGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatgaatg                    <  1:180653/146‑1 (MQ=255)                                                                                                                                                ttttATGCGGGAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCACAATGAATGTTaaa               <  2:192385/150‑1 (MQ=255)                                                                                                                                                  ttATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACgg            >  1:533572/1‑151 (MQ=255)                                                                                                                                                  ttATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACgg            >  1:549353/1‑151 (MQ=255)                                                                                                                                                          gCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTaa     >  2:539969/1‑150 (MQ=255)                                                                                                                                                            gAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAAACt  >  1:66389/1‑151 (MQ=255)                                                                                                                                                            |                                                                                                                                                        TTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGG‑ATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCC‑CTTGTT‑ACAGTTGTGTACAAGGGGC‑C‑TGATTTTTATGACGGCGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAAACT  >  NC_000913/1622666‑1622966

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑