Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,622,816	0	G	A	41.7%	34.8 / 42.0	48	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
Reads supporting (aligned to +/- strand):  ref base G (24/4);  new base A (0/20);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.27e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAAACT  >  NC_000913/1622667‑1622966                                                                                                                                                          |                                                                                                                                                       tttATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCg                                                                                                                                                        >  1:796543/1‑150 (MQ=255)  ttATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGa                                                                                                                                                       <  1:209337/150‑1 (MQ=255)    aTGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGaaa                                                                                                                                                     >  1:760567/1‑150 (MQ=255)       gCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGaaaaaa                                                                                                                                                  >  1:26798/1‑150 (MQ=255)         cGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAAc                                                                                                                                               <  2:758373/151‑1 (MQ=255)           tACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCg                                                                                                                                             >  2:658542/1‑151 (MQ=255)            aCTTGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACATTTGTGTACAAGGGTCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCg                                                                                                                                             <  2:938455/150‑1 (MQ=255)             cTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCg                                                                                                                                             <  2:684177/149‑1 (MQ=255)              tGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGcc                                                                                                                                           >  1:818665/1‑150 (MQ=255)                      attttattttCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACcg                                                                                                                                  >  2:239853/1‑151 (MQ=255)                       ttttttttttTGTTTTTCGGGCCGCTTATTGCAGCCCCAAATGGAAGTAATAAGAAGCGCGGATAACCCCTCCCCT‑ACCCGCCCCTTATTAACGGTGTTGTACAGGGGGCT‑TTT‑TTTTTATGA‑GGGAAAAAAAAAACCGCCAGTAAACcg                                                                                                                                  <  2:368695/150‑1 (MQ=255)                       tttttttttCTGTTTTTCTGGCCGTGTTTTCCAGCCAAAAGGGGGATGACAAAGGAAGGGAAAAAACCCCCCCCCAACCCGCCCCTTTGTT‑ACATTTGGGAACAGGGGCCT‑TTT‑TTTTTAGGC‑CGGAAAAAAAAAACCGCCAGTAAACcg                                                                                                                                  <  1:27664/150‑1 (MQ=255)                        tttattttCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACcggc                                                                                                                                >  1:784292/1‑151 (MQ=255)                          tattttCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACcggcg                                                                                                                               >  1:377928/1‑150 (MQ=255)                            ttttttggtttcctgcCCGCTTTTTTCACCCAAAAAGGGGATGATTAAGGAAGGGAAATATCCCCTCACCCACCCGCCCTTTTTTT‑CCGTTTGGGAAAGGGGGGCG‑TGT‑TTTTAAGGA‑GGGAAAAAAAAAACCGCCAGTAAACcggcg                                                                                                                               <  2:416309/148‑1 (MQ=255)                                 tttttttctggCCGCGTATTCCACCCAAAAATGGGATAATTAATGAGCGAAGATACCCCCCCCCCTACCCGCCCCTTTGTT‑ACATTTGTGAAAAGGGGACT‑TTT‑TTTTTATGG‑CGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAAt                                                                                                                         <  1:534812/146‑1 (MQ=255)                                  ggttttctggCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCt                                                                                                                      >  1:327112/1‑151 (MQ=255)                                   tttttctggCCGTTTATTTCACCCAAAAATGGGATGAAAAATGAAGGGAGAAAACCCCCCCCCTACCCGCCCCTTTTTT‑ACAGTTGTG‑AAAAGGGGCCTTTT‑TTTTTAGGA‑CGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAAt                                                                                                                         <  1:683740/146‑1 (MQ=255)                                     tttctggTCGCGAATTACAGCCACAATGGGGACGACTAATGAGCGGAGATAATCCCTCACCTAACCAGCACCTTGGT‑ACAGATGGGTACAAGGGGAC‑TGA‑CTTGTACGC‑CGGCGAAAAAAAACCGCCAGTAGACtggcggcaaattgatcg                                                                                                                   >  2:969734/1‑140 (MQ=255)                                          ggccgttttttccAGCCAAAAATGGGATGATTAATGAAGGGAAATAACCCCTCCCCAACCCGCCCCTTTTTT‑ACATTTGTGTAAAGGGGGCT‑TTT‑TTTTTAGGA‑CGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCAt                                                                                                                 <  1:1054916/136‑1 (MQ=255)                                             cgcgTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGAt                                                                                                             >  2:560443/1‑149 (MQ=255)                                              gcttATTCCACCCAAAAATGGGATGACTAATGAACGGAAAAAACCCCTCCCCTACCCGCCCCTTTTTT‑ACAGTTGTGTA‑AAGGGGCCTTTT‑TTTTTAGGA‑GGGCAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGa                                                                                                          <  1:120964/148‑1 (MQ=255)                                              gcgTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATACTCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGACTGGAt                                                                                                             >  2:650398/1‑148 (MQ=255)                                              gcgTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGAt                                                                                                             >  1:951364/1‑148 (MQ=255)                                               cgTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGAt                                                                                                             >  1:759127/1‑147 (MQ=255)                                                 tATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGAttt                                                                                                       >  2:379838/1‑151 (MQ=255)                                                  ctttCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGAttt                                                                                                       >  2:565148/2‑150 (MQ=255)                                                       acccAAAAAGGGGATGAATAAGGAACGGAGATATCCCCCCCCCAACCCGCCCCCTTGTT‑ACATTTG‑GAAAAAGGGGGC‑TTT‑TTTTTTAGACCGGAAAAAAAAATCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGtt                                                                                                  <  2:876946/148‑1 (MQ=255)                                                         ccAAAAAGGGAATCACTATTGAGGGGAAATACCCCCCCCCCAACCCGCCCCTTTGTT‑AATGTGGTGAACAGGGGGCC‑GTT‑TTTTTAGGC‑CGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGttt                                                                                                 <  1:790000/149‑1 (MQ=255)                                                           aaaagtGGGATGAAAAAAAAAAGGAAAAAACCCCCCCCCGACCCGGCCCTTGGTT‑ACGTTTGTGAAAGGGGTGCC‑TTT‑TTTTTAGGG‑CGAAAAAAAAAAGCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGtttt                                                                                                <  1:769071/143‑1 (MQ=255)                                                           aaaaaTGGGAGGAAAAATGAGGGAAGATAACCCCCCCCCTACCCGCCCCTTTTTT‑ACATTTGTGAAAAGGGGGCT‑TGT‑TTTTTAGGA‑GGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTtgtg                                                                                                    <  1:904632/142‑1 (MQ=255)                                                           aaaaaGGGAATGACAAATAAACGGAAATAACCCCCCCCCAACCCGGCCCCTTTTT‑CCTGTTGTGAAC‑AGGGGGC‑TGATTTTTTAGGG‑CGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGc                                                                                              <  2:837779/148‑1 (MQ=255)                                                                tGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTAc                                                                                        >  1:807519/1‑151 (MQ=255)                                                                       aCTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTaa                                                                                   >  1:690277/1‑149 (MQ=255)                                                                          agggAAGGGAGATACTCCCTCACCGAGCCGGCCCTTTGTT‑ACGGGGGTTTACAGGGGGGT‑TTT‑TTTTAATGA‑CGGAAAAAAAAATCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTa                                                                                    <  2:537013/142‑1 (MQ=255)                                                                                 ggAGATACCCCCTCACCTACCCGCCCCTTTGTT‑ACATTTGTACAAAGGGGGCC‑TTT‑TTTTTATGC‑GGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTcc                                                                       <  1:636516/151‑1 (MQ=255)                                                                                  gaaaTAACCCCTCCCCAACCCGCCCCTTTGTT‑ACATTTGTGCAAAGGGGGCT‑TGT‑TTTTTATGA‑CGGGAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCa                                                                             <  1:1024563/141‑1 (MQ=255)                                                                                     aTAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGc                                                                    >  1:702581/1‑150 (MQ=255)                                                                                                ccaacccGGCCCTTTTTT‑ACATTTGTGAACAGGGGCCT‑TTT‑TTTTTAGGA‑CGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATaa                                                            <  1:532299/142‑1 (MQ=255)                                                                                                   acccGGCCCTTTTTA‑ACAGTTGTGTAAAGGGGGCT‑TTT‑TTTTTATGA‑CGAAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATc                                                      <  1:810015/148‑1 (MQ=255)                                                                                                     ccGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACCCTAACAGGCATTTTCCTGCACTGATAACGAATCGtt                                                   >  1:877603/1‑151 (MQ=255)                                                                                                         ccccTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGac                                                >  1:815922/1‑150 (MQ=255)                                                                                                                       ttGTGAAAAGGGGGCT‑TGT‑TTTTTATGA‑CGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCa                                    <  1:785943/149‑1 (MQ=255)                                                                                                                           gtACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGtttt                               >  2:722680/1‑150 (MQ=255)                                                                                                                             aCAAGGGGCC‑TGA‑TTTTTATGC‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtctc                            >  2:965095/1‑151 (MQ=255)                                                                                                                                            tttttATGA‑CGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGtt                  <  1:958964/148‑1 (MQ=255)                                                                                                                                               ttAGGA‑CGACAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACg             <  1:659085/150‑1 (MQ=255)                                                                                                                                                      cGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCtt       >  1:210796/1‑150 (MQ=255)                                                                                                                                                         cGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACCGAGCTTAAAc   >  1:831698/1‑151 (MQ=255)                                                                                                                                                          gAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAAACt  >  2:384542/1‑151 (MQ=255)                                                                                                                                                          |                                                                                                                                                       TTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGA‑TTTTTATGA‑CGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAAACT  >  NC_000913/1622667‑1622966

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑