Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,622,816	0	G	A	51.1%	3.9 / 67.5	47	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
Reads supporting (aligned to +/- strand):  ref base G (21/2);  new base A (0/24);  total (21/26)
Fisher's exact test for biased strand distribution p-value = 2.02e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.17e-03

TTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAAA  >  NC_000913/1622668‑1622964                                                                                                                                                          |                                                                                                                                                      ttATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGa                                                                                                                                                      >  1:594321/1‑150 (MQ=255)  tATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGaa                                                                                                                                                     >  1:242965/1‑150 (MQ=255)     ggCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGaaaaa                                                                                                                                                  >  1:679536/1‑150 (MQ=255)         gTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑cc                                                                                                                                            >  2:357729/1‑151 (MQ=255)         gTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑cc                                                                                                                                            <  2:871019/151‑1 (MQ=255)             tGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGcc                                                                                                                                         >  2:365767/1‑150 (MQ=255)               ggAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGt                                                                                                                                      >  1:140035/1‑151 (MQ=255)                      ttttattttCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACcgg                                                                                                                               >  2:914901/1‑151 (MQ=255)                       tttattttCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACcgg                                                                                                                               >  1:339189/1‑150 (MQ=255)                        tttttttctgtttttctggCCGCTTTTTCCACCAAAAAAGGGGATGACTAATAAAGGAAAATACCCCCCCCCCTACCCGCCCCTTT‑TTTACA‑GTTGTGTACAAGGGGCT‑TGT‑TTTTTATGACGG‑CAAAAAAAAA‑CCGCCAGTAAACcggc                                                                                                                              <  1:168591/147‑1 (MQ=255)                           ttttctggttttctggCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGt                                                                                                                           >  2:305902/1‑150 (MQ=255)                           tgttgtgtttttcgggCCGATTATTACACACAAAAGGGGGATGAAAAATGAGGGGAAAAAACCCCTCA‑CAAACCGGCCCCTTGGTTAGA‑TTTG‑GGAAAGGGGGCCTTGT‑TTTTTAGGACGA‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGt                                                                                                                           <  2:113674/142‑1 (MQ=255)                            tttttgtttttcgggCCGCTTATTCCACCCAAAAAGGGGATGAATAATGAAGGGA‑AAAAACCCCCCCCCAACCCGCCCCTT‑TTTAAATGTTGTGAACAGGGGCCC‑TGT‑TTTTTATGCCGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTg                                                                                                                          <  1:909710/150‑1 (MQ=255)                              tctggttttctggCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGaa                                                                                                                        >  1:546514/1‑150 (MQ=255)                                 gtttttcgggCCGGTTTTTTCACCAAAAAAGGGGATAAATAATGAACGGAAATAACCCCTCCCCTACCCGCCCCCTT‑GTACCG‑GTGGTGCACAGGGGGCT‑TGT‑TTTTTGGGACGG‑CAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGc                                                                                                                     <  1:554708/148‑1 (MQ=255)                                  gttttctggCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCtt                                                                                                                   >  1:732063/1‑151 (MQ=255)                                   ttttctggCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCtt                                                                                                                   >  2:389026/1‑150 (MQ=255)                                        tggCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATgg                                                                                                             >  1:643774/1‑151 (MQ=255)                                         gcccGCTTTTTTCACCAAAAAAGGGGATGACAAATGAAGGGAAATACCCCCTCCCCTACCCGCCCCTTT‑TTTACG‑TTTGTGTAAAGGGGGCC‑TGT‑TTTTTAGGACGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCAt                                                                                                               <  1:99563/146‑1 (MQ=255)                                         gcccGCTTATTCCACCCAAAAAGGGGATGTCAAATGAAGGGAGATACCCCCCCCCCAACCCGCCCCTTT‑TTTAAT‑GTTGTGAAAAAGGGCCT‑TGT‑TTTTTATGAGGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGa                                                                                                            <  2:89593/149‑1 (MQ=255)                                               ttATTCCAGCAAAAAAGGGGAAGACAAAGGAGAGGAGAAATTCCCCCACCTACCCGCCCTTTT‑TTTAGG‑GTTGTAAAAAAGGGGCT‑TGT‑TTTTTAGGGGGGAAAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAg                                                                                                         <  1:22816/148‑1 (MQ=255)                                                      acccAAAAAGGGGATAACTAAGGAACGGAAATACCCCCCCCCCAACCCGCCCCTTT‑TTTAAA‑GTTGTGTACAGGGGGCT‑TTT‑TTTTTATGACGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGtt                                                                                                <  1:119749/148‑1 (MQ=255)                                                           aaaaGGGGATGACTAATAAACGAAAATACCCCCTCCCCAACCCGCCCCTTT‑TTTACG‑TTTGTGTAAAGGGGGCT‑TTT‑TTTTTAGGACGG‑CAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTg                                                                                             <  1:747251/147‑1 (MQ=255)                                                            aagtGGGATAACAAATGAACGAGAAAAACCCCTCCCCTACCCCGCCCCTT‑TTTAAA‑TTTGTTTACAAGGGCCT‑TTT‑TTTTTAGCACGG‑AAAAAAAAAT‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCttt                                                                                         <  2:758904/148‑1 (MQ=255)                                                            aaaTGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCttt                                                                                         >  1:157548/1‑151 (MQ=255)                                                             aaggggATGAAAAATGACGGGAAAAAACCCCCCCCCTACCCGCCCCTTT‑TTTACG‑GTTGTGTACAGGGGGCT‑TTT‑TTTTTATGACGG‑GAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCtttt                                                                                        <  1:304861/148‑1 (MQ=255)                                                                gggAAGAATAATAAACGGATAAACCCCCCCACCTACCCCCCCCTTT‑GTTATG‑GTGGTTAACAAGGGGCT‑TGT‑TTTTGATGAGGA‑CAAAAAAAAT‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCtttt                                                                                        <  2:506328/148‑1 (MQ=255)                                                                   aTGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCt                                                                                   >  1:756864/1‑150 (MQ=255)                                                                         aaTAAAGGGAAATAACCCCTCCCCAACCCGCCCCTTT‑TTTACA‑TTTTTG‑AAAAGGGGCCTTTT‑TTTTTAGGCGGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAg                                                                              <  1:692412/149‑1 (MQ=255)                                                                             aaCGGAAATACCCCCCCCCCTACCCGCCCCTTT‑GTTAGG‑TTTGTGTACAGGGGGGG‑TGT‑TTTTTAGGAGGG‑AAAAAAAAAT‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACa                                                                               <  2:37782/144‑1 (MQ=255)                                                                                  aaaaaccccccCACCTACCGGCCCCCTT‑TTTACA‑G‑TGTTTAACAGGGGCCTTGT‑TTTTTATGGCGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCAtttt                                                                       <  1:937981/140‑1 (MQ=255)                                                                                             caccgccccGTCCCTTT‑GTTGCA‑GTTGTGTACAAGGGGCT‑TGT‑TTTTTTTGACGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACg                                                        <  1:598467/144‑1 (MQ=255)                                                                                               ccaacccGGCCCTTT‑TTTACT‑GTTGTGTAAAAGGGTCT‑TTT‑TTTTGATGAGGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACg                                                        <  2:772904/144‑1 (MQ=255)                                                                                                    ccGCCCCTTT‑TTTACA‑TTTGTGTAAAGGGGCCC‑TTT‑TTTTTAGGGGGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAAt                                                     <  1:680077/147‑1 (MQ=255)                                                                                                                       ttGTGTAGAAGGGGCT‑TGT‑TTTTTAGGACGA‑CAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATc                                   <  2:620522/148‑1 (MQ=255)                                                                                                                         gtgtACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGttt                              >  1:256410/1‑151 (MQ=255)                                                                                                                             aaaaGGGGCC‑TTTTTTTTTAGGACGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtct                           <  1:684662/149‑1 (MQ=255)                                                                                                                             aCAGGGGGCT‑TGT‑TTTTTAGGGCGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtc                            <  2:643766/149‑1 (MQ=255)                                                                                                                              cAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtctc                          >  2:587303/1‑150 (MQ=255)                                                                                                                              acaGGGGGC‑CGA‑TTTTTTAGACGG‑AGAAAAAAAATCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtc                            <  2:944703/147‑1 (MQ=255)                                                                                                                                aGGGGCCTTTA‑TTTTTAGGAGGG‑AAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGtttt                             <  1:608465/146‑1 (MQ=255)                                                                                                                                     cc‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatgaatg                  >  1:825493/1‑151 (MQ=255)                                                                                                                                            tttttATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTaa              >  1:929308/1‑150 (MQ=255)                                                                                                                                            tttttAGGACGG‑CAAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTaa              <  1:770179/150‑1 (MQ=255)                                                                                                                                            tttttAGAACGG‑CAAAAAAAAG‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTaa              <  1:701517/150‑1 (MQ=255)                                                                                                                                                tATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAAc            >  2:305546/1‑148 (MQ=255)                                                                                                                                                         cGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTaaa  >  1:6779/1‑150 (MQ=255)                                                                                                                                                          |                                                                                                                                                      TTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTT‑GTTACA‑GTTGTGTACAAGGGGCC‑TGA‑TTTTTATGACGG‑CGAAAAAAAA‑CCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAAA  >  NC_000913/1622668‑1622964

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑