Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,622,816	0	G	A	42.5%	21.3 / 40.9	40	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 (0/17);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 1.93e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGG  >  NC_000913/1622666‑1622956                                                                                                                                                            |                                                                                                                                             ttttATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCg                                                                                                                                              >  2:660733/1‑151 (MQ=255)       ggCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGaaaaa                                                                                                                                         >  2:288223/1‑150 (MQ=255)            tACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCg                                                                                                                                   >  2:975566/1‑151 (MQ=255)                gggAATAATTTTATTTTCTGTTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTACCCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCa                                                                                                                                <  2:557541/150‑1 (MQ=255)                  gAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGt                                                                                                                              >  2:348094/1‑150 (MQ=255)                      aatTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGTCGGCGAAAAAAAACCGCCAGTAAAc                                                                                                                          >  1:834968/1‑150 (MQ=255)                      aatTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAAcc                                                                                                                         >  1:835620/1‑151 (MQ=255)                       attttattttCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAAcc                                                                                                                         >  2:430123/1‑150 (MQ=255)                          tttttttctttttttcggcCCGCTTTTTCCACCCAAAAATGGAATG‑ATTAAGGAACGGAAATACCCCCCCCCCAACCCGCCCCT‑TTTTTACTTTTGT‑AAAAAGGGGCCTTTT‑TTTTT‑AGGCCGGAAAAAAAAAACCGCCAGTAAACcggc                                                                                                                      <  2:160732/147‑1 (MQ=255)                              tttctggtttgctggCCGTTTTTTTCACCCA‑AAAGGGGAAGAACAAAGAAACGGAAAAACCCCCTCCCCTACCCGCCCCT‑TTTTTACGGTTGTGAACAGGGGGCT‑TGT‑TTTTT‑ATGACGGAAAAAAAAAACCGCCAGTAAACCGGCGGTg                                                                                                                  <  1:75347/150‑1 (MQ=255)                                    gttttctggCCGCGTATTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCtt                                                                                                           >  1:542772/1‑151 (MQ=255)                                        tcgggCCGCTTTTTACAGCCAAAAGGGGGATA‑AATAATGAGCGGAAATACCCCCCCACCAACCCGCCCCT‑TTTTTACGGTTGTGAAAAGGGGGCT‑TTT‑TTTTT‑ATGAGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTg                                                                                                          <  1:1019337/145‑1 (MQ=255)                                             ccGTGTATTTCACCCAAAAGGGGGATA‑AAAAAGGAAGGGAAATACCCCCTCACCAAACCGCCCCT‑TTTTTACAGTTGTGAAAAGGGGGCT‑TTT‑TTTTT‑AGGAGGGCAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTg                                                                                                          <  1:589021/143‑1 (MQ=255)                                                 tttttccaccaaaaaaGGGGATA‑ACTAAGGAGGGGAAATAACCCCCCCCCAACCCGCCCCT‑TTGTTACATTTGGGTACAGGGGGCT‑TGT‑TTTTT‑ATGAGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGAt                                                                                                   <  2:332956/133‑1 (MQ=255)                                                   aTTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGAttt                                                                                             >  2:1013540/1‑150 (MQ=255)                                                           cacaAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTg                                                                                     >  2:310199/1‑150 (MQ=255)                                                                 tGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTAc                                                                              >  1:985310/1‑151 (MQ=255)                                                                    gaataaatAATGAAGGAAAATAACCCCCCCCCTACCCGCCCCT‑TTTTTACGTTTGTGAAAAGGGGGCT‑TTT‑TTTTT‑AGGAGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTa                                                                               <  1:769311/141‑1 (MQ=255)                                                                            aaTGAAGGGAGATACCCCCTCCCCTACCCGCCCCT‑TTGTTACTTTTGTGTAGAGGGGCCT‑TTT‑TTTTT‑ATGGGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGc                                                                    <  2:342961/151‑1 (MQ=255)                                                                                    gagaTAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCt                                                            >  1:284359/1‑151 (MQ=255)                                                                                           cccccccccTACCCGCCCCT‑TTTTTACGGTTGTGAAAAGGGGGCT‑TTT‑TTTTT‑AGGCGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGa                                                     <  2:608579/144‑1 (MQ=255)                                                                                             ccccccccaaCCCGCCCC‑TTTTTAACGTTTTGGAAGAGGGGTC‑TTTTTTTTT‑AGGACGGAAAAAAAAACCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCa                                                         <  1:843066/138‑1 (MQ=255)                                                                                             cccccccaaaCCGGCCCCTTTGTTCCGGTTGTG‑AAAAGGGGCC‑TTA‑TTTTTAATGGGGGAAAAAAAAATCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCt                                                            <  1:708899/135‑1 (MQ=255)                                                                                                ccccaacccGCCCCT‑TTTTTACAGTTGTGTACAGGGGGCT‑TTT‑TTTTT‑AGGCGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACg                                                <  2:877489/144‑1 (MQ=255)                                                                                                     acccGCCCCC‑TTTTTACTGTTGTGAAAAGGGGGCT‑TTT‑TTTTT‑AGGAGGGCAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAAt                                             <  2:732524/147‑1 (MQ=255)                                                                                                      cccGCCCCT‑TTGTTAAGGTTTTGAACGGGGGGCT‑TAT‑TTTTT‑AGAACGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGaa                                              <  1:909420/146‑1 (MQ=255)                                                                                                                  gTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGt                                 >  2:42412/1‑149 (MQ=255)                                                                                                                     tacttttgtgcaaaGGGGCC‑TTTTTTTTT‑ATGAGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAg                                  <  1:288108/134‑1 (MQ=255)                                                                                                                       aGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATc                           >  1:6951/1‑150 (MQ=255)                                                                                                                         ttGTGTAAAAGGGGCC‑TGA‑TTTTT‑ATGACGGAGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCa                          <  2:952589/149‑1 (MQ=255)                                                                                                                                 aaGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCa                 >  2:902510/1‑150 (MQ=255)                                                                                                                                   ggggCC‑TTT‑TTTTT‑ATGGCGAAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGttt                      <  2:910293/143‑1 (MQ=255)                                                                                                                                       ggcttttttttt‑AGGGCGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatgaa            <  1:975281/144‑1 (MQ=255)                                                                                                                                          tGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGtt        >  1:71186/1‑151 (MQ=255)                                                                                                                                           gA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGtt        >  2:368169/1‑150 (MQ=255)                                                                                                                                            a‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTa       >  1:417898/1‑150 (MQ=255)                                                                                                                                                ttt‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACg   >  2:387030/1‑151 (MQ=255)                                                                                                                                                 tt‑ATGACGGAAAAAAAAACCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACg   <  1:570986/150‑1 (MQ=255)                                                                                                                                                  t‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACgg  >  2:697426/1‑150 (MQ=255)                                                                                                                                                  t‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACgg  >  1:854560/1‑150 (MQ=255)                                                                                                                                                          gCGAAAAAAAACCGCCAGTAAACCGAAGGTGAAATTTTCCATGGATACGGTTGCGTATAGCTTTTAATCTCAGAGGATTTTTACCGCAGTGATAACGGAGCAATGACCCAGTATCAACCGATTTCTCACAGTAAGATAAACgg  >  1:298680/1‑143 (MQ=255)                                                                                                                                                            |                                                                                                                                             TTTTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATG‑ACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCC‑TTGTTACAGTTGTGTACAAGGGGCC‑TGA‑TTTTT‑ATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGG  >  NC_000913/1622666‑1622956

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: ‑