Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,287,719	0	T	A	43.5%	58.1 / 24.5	47	intergenic (‑348/‑45)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
Reads supporting (aligned to +/- strand):  ref base T (23/3);  new base A (0/20);  total (23/24)
Fisher's exact test for biased strand distribution p-value = 6.32e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAAAGAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCG  >  NC_000913/4287569‑4287860                                                                                                                                                       |                                                                                                                                               aaaaaGAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAAt                                                                                                                                                >  1:881834/1‑151 (MQ=255)        ggAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑cc                                                                                                                                        >  2:634279/1‑151 (MQ=255)            gATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGcc                                                                                                                                     >  1:480177/1‑150 (MQ=255)                  gACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGca                                                                                                                               >  1:869959/1‑150 (MQ=255)                      aaCTCAAAAGTGTTATTTTACATGCACTTACAATTGAGTAAAGACAACATTCACGGTGTGTTTTTTTTTTACACATAGGGACGAGAAATGTCATGCCAGGGTAGGTGCGGTTACTGGCGTAAAAAACAATAAAAC‑CCGCCATTGc                                                                                                                                <  2:121050/145‑1 (MQ=255)                            aatgtgtTATTTTACATGCCTTTAAATTTGATTAAAGACAACATTCACAGTGTGTTTATTTTTTACACATGGGGGCAACAAATGTCAGGACAGTGTAGGTGCGGTTACGGTTGTAAAAAACAAAAAAAA‑CCGCCATTGCAACAATGGCGCa                                                                                                                    <  2:779063/148‑1 (MQ=255)                                    aTTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGAt                                                                                                            >  1:165660/1‑151 (MQ=255)                                                   aCAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGAc                                                                                              >  1:571368/1‑150 (MQ=255)                                                     aaTTGATTAAAGAAAACATTCACGGTGGGTTTATTTGTTACACAAAGGGGCGAGCAATTTCATGACGGTGTGGGTGCGGTTACTGTAGTGAAAAAAAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACaa                                                                                            <  2:890809/150‑1 (MQ=255)                                                           ttAAAGAAAACATTCACAGTGTGGTTTTTTGTTACCCATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATaa                                                                                      <  2:377986/150‑1 (MQ=255)                                                           ttAAAAAAAACATTCACATTTTGTTTATTTTTTACACATAGGGGCAAACAATTTAATGACATTGTAGGTGCGGTTACTGTGGTAAAAAAAAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATaa                                                                                      <  2:315217/150‑1 (MQ=255)                                                            tAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATaaa                                                                                     >  1:823724/1‑150 (MQ=255)                                                             aaggaaaacaTTCACGGTTTGTTTATTTGTTCCCCATGGGGGCGAAAAATGCCAGGACGGTTTAGGGGCGGTTGCGGTCGGAAAAAACAAAAAAAG‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATaaaaa                                                                                   <  2:672220/145‑1 (MQ=255)                                                              aaGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAAt                                                                                  >  1:699241/1‑151 (MQ=255)                                                                 acaacaTTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATaa                                                                                <  1:148636/150‑1 (MQ=255)                                                                   aacaTTCACAGTGTGGTTATTTGTTACACATGGGGGCGAGAAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTAAAAAACAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAac                                                                              <  2:7591/150‑1 (MQ=255)                                                                   aacaTCCACATTGTGGTTTTTTGTTACACAAAGGGGCGAGAAAGGTCATGACAGTGTAGGTGGGGTTACTGTCGTAAAAAACAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAac                                                                              <  2:673029/150‑1 (MQ=255)                                                                     caTTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAacgc                                                                            >  2:363662/1‑150 (MQ=255)                                                                     caTTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAacgc                                                                            >  2:586656/1‑150 (MQ=255)                                                                           caGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGt                                                                     >  2:302311/1‑151 (MQ=255)                                                                              tgtgGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATc                                                                  >  1:548729/1‑151 (MQ=255)                                                                                      ttttttACACAAAGGGGCGAGAAATGACATAACAGGGTAGGTGCGTTTACTGCCGTAAAAAACAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAg                                                             <  2:810904/148‑1 (MQ=255)                                                                                       ttttacctcaTGGGGGCAATCATTGTCTTGCCAGTGGGGGTGCGTTTGCTTTCTGAAAAAACAAAAAAAC‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAGGGCTAAAAATAAACGCACGCCGTATCtt                                                                <  2:617233/136‑1 (MQ=255)                                                                                          ttACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTg                                                      >  2:124215/1‑151 (MQ=255)                                                                                          ttACAAATAGGGGGGAGAAATGTCTGGAAAGTGTAGGTGGGTTTTTTGCCGTAAAAAAAAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTAt                                                        <  1:654876/149‑1 (MQ=255)                                                                                           tACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTg                                                      >  1:569601/1‑150 (MQ=255)                                                                                            acacAGAGGGGCGAAAAATGACATGACAGTGTGGGGGGGTTGAGTGGGGGAAAAAACAAGAAAAA‑CCGGCATGGCAACAATGGCGCAATTCGGATGAAGCCGGTATGACAAGGATAAAAATAAGCGCGCGCCGTATCTTCAGCTTGTTGAt                                                    <  2:169929/151‑1 (MQ=255)                                                                                                aagggggggAGAAATGTAAGGACAGTGTAGGTGCGTTTACTGTGGTAAAAAAAAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTcc                                                 <  2:376784/147‑1 (MQ=255)                                                                                                  aGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCttt                                              >  1:730645/1‑151 (MQ=255)                                                                                                     ggCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCtttttt                                           >  2:532804/1‑151 (MQ=255)                                                                                                        gagaAATGTCATGACGGGGTAGGGGCGTTTACTGTGGAAAAAAAAAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCtttttt                                           <  2:494024/148‑1 (MQ=255)                                                                                                        gAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttctt                                        >  2:184015/1‑151 (MQ=255)                                                                                                        gAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttctt                                        >  1:235098/1‑151 (MQ=255)                                                                                                        gAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttctt                                        >  2:678629/1‑151 (MQ=255)                                                                                                               gTCATGACAGTGTAGGTGGGTTTACTGTCGGAAAAAAAAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCa                                   <  1:755726/149‑1 (MQ=255)                                                                                                                   tGACGGTGTGGGGGGGTTTATTGGGGTAAAAAAAAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACt                                 <  1:615578/147‑1 (MQ=255)                                                                                                                   gaccAGTGGGGGTGCTGTTACGGTGATAAAAAAAAAAAAAAA‑CCTCCATTGCAACAATGGCGCAATTCTGTTGAAGCCCCTATGACAAGGATAAAAATAACCGCACGCCGTATCTTCAGCTTATTGATTCCTtttttctttt                                      <  2:799520/139‑1 (MQ=255)                                                                                                                     aCAGCGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGtt                           >  1:53245/1‑151 (MQ=255)                                                                                                                         tgtAGGGGGGGTACCTGTCTGAAAAAACAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAATGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCAc                        <  2:690147/150‑1 (MQ=255)                                                                                                                          gtgggggCGGTTACTTTCTTAAAAAAAAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTc                          <  2:881625/141‑1 (MQ=255)                                                                                                                             ggTCCGGTTACTGTC‑AAAAAAACAAAAAAAATCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACg                       <  2:279607/147‑1 (MQ=255)                                                                                                                                  ggTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACaa               >  1:799217/1‑150 (MQ=255)                                                                                                                                    ttcctttggtaaaaaaaaaaaaaaa‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAAc             <  1:281659/139‑1 (MQ=255)                                                                                                                                      attGTCGTAAAAAAAAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACgg           <  2:863666/148‑1 (MQ=255)                                                                                                                                       gagtggTGAAAAAAAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATGCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAAc             <  2:120436/142‑1 (MQ=255)                                                                                                                                        tGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGgctg        >  1:383916/1‑151 (MQ=255)                                                                                                                                        tGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGgctg        >  1:188721/1‑151 (MQ=255)                                                                                                                                          tgttaaaaaaCAAAAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTGTTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGgct         <  1:282708/143‑1 (MQ=255)                                                                                                                                           cGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTc     >  2:723714/1‑151 (MQ=255)                                                                                                                                               aaaaaaaaaaaaaa‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGgct         <  1:372538/143‑1 (MQ=255)                                                                                                                                               aaaaaaaaaaaaaa‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCg  <  2:452850/150‑1 (MQ=255)                                                                                                                                               aaaaaaaaaaaaaa‑CCGCCATTGCAACAATGGCCCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGgctgct      <  2:615329/146‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                               AAAAAGAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCG  >  NC_000913/4287569‑4287860

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑