Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,287,719	0	T	A	42.5%	63.8 / 22.7	47	intergenic (‑348/‑45)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
Reads supporting (aligned to +/- strand):  ref base T (22/5);  new base A (0/20);  total (22/25)
Fisher's exact test for biased strand distribution p-value = 9.41e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAAAGAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCGCAAAACCTG  >  NC_000913/4287569‑4287869                                                                                                                                                        |                                                                                                                                                       aaaaaGAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAAt                                                                                                                                                        <  2:54867/151‑1 (MQ=255)    aaGAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATaaa                                                                                                                                                     <  2:289522/151‑1 (MQ=255)       agGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAAc                                                                                                                                                  <  2:101403/151‑1 (MQ=255)              tACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCAtt                                                                                                                                           >  2:658622/1‑151 (MQ=255)                  gACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGca                                                                                                                                        >  2:369140/1‑150 (MQ=255)                        ctctAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATgg                                                                                                                                 >  2:668946/1‑151 (MQ=255)                            aaaGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGgcgc                                                                                                                              >  2:660345/1‑150 (MQ=255)                                 ggTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGGGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAAtt                                                                                                                          <  2:631983/149‑1 (MQ=255)                                       ttACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGa                                                                                                                   >  1:599015/1‑150 (MQ=255)                                          cATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGcc                                                                                                               >  1:749398/1‑151 (MQ=255)                                               aCTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTAt                                                                                                          >  1:142105/1‑151 (MQ=255)                                               aCTTACAATTGATTAAAGACAACATGCACAGGGGGGTTATTTGTTACAAATGGGGGCGAGCAATGTAATGACAGTGTAGGTGC‑GGTTACTGTGGTAAAAAACAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCt                                                                                                            <  1:242334/149‑1 (MQ=255)                                                   aCAATTGATAAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGATCAATGTCATGACGGTTTAGGTGC‑GGTTCCTGTCGTGAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATg                                                                                                         <  1:591153/148‑1 (MQ=255)                                                     aaTTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACa                                                                                                      >  1:387298/1‑149 (MQ=255)                                                          ataaaaGACAACATTCACAGTGTGGTTATTTGTTACACATGGGGGCGAGAAATATCATGACAGTGTAGGGGC‑GGTTACTGTCGTGAAAAAAAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATa                                                                                                <  1:167560/147‑1 (MQ=255)                                                          ataaaaGACAACATTCAAAGTGTGGTTTTTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GTTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGAt                                                                                                 <  2:321090/146‑1 (MQ=255)                                                           ttAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATaa                                                                                               >  2:93178/1‑150 (MQ=255)                                                           ttAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATaa                                                                                               >  2:284832/1‑150 (MQ=255)                                                               aGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGCAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGCTAAAAAt                                                                                           >  1:231531/1‑150 (MQ=255)                                                                   aacaTTCACAGTGTGTTTATTTGTTACACATAGGGGCGAGAAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAac                                                                                       <  2:748335/150‑1 (MQ=255)                                                                       ttCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAacgcacg                                                                                  >  2:576114/1‑151 (MQ=255)                                                                        tCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAacgcacgc                                                                                 >  1:873603/1‑151 (MQ=255)                                                                         cccggtgtGATTTTTGTTTAAACATGGGGGGGAACAATTCCAGGACGGTGTAGTTGC‑GGTTCATGTCGGAAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGcc                                                                                <  2:385393/147‑1 (MQ=255)                                                                         cacaGTGTGGTTATTTGTTACACATAGGGGCGAGCATTGTCAGGCCAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAacgcac                                                                                   <  1:602212/148‑1 (MQ=255)                                                                                tgGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCCGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCAGTATCtt                                                                         >  1:696617/1‑151 (MQ=255)                                                                                 gttttttttttACACATAGGGGCGAGAAATTTCATGACAGTGTGGGTGC‑GTTTCCTGTCGTAAAAAACAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTa                                                                             <  2:732571/141‑1 (MQ=255)                                                                                      tttttaacccaTGGGGGCGAGAATTTTCATGAAAGTGTAGGTGC‑GGTTACTGTCGTAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAg                                                                      <  2:593508/139‑1 (MQ=255)                                                                                      tttGTAACAAAGAGGGGCGAAAAATGTCATGAC‑GTGGTAGTGCTGTTTATTGTCGAAAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGc                                                                     <  1:252805/149‑1 (MQ=255)                                                                                              acaTGGGGGGGAGAAATGTCATGACAGTGTAGGTGG‑GTTTCCTGTCGTAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGa                                                              <  2:594803/148‑1 (MQ=255)                                                                                                aTAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCt                                                         >  2:684431/1‑151 (MQ=255)                                                                                                  gggggCGAAAAATGTAATGACATTGTAGGGGC‑GTTTCTGGCCGTAAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCttt                                                       <  1:653328/150‑1 (MQ=255)                                                                                                  aGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCttt                                                       >  2:787674/1‑151 (MQ=255)                                                                                                    gggCGAGAATTGTCATGACAGTGTGGGTGG‑GTTTCCTGTCGTAAAAAACAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCttttt                                                     <  2:871179/151‑1 (MQ=255)                                                                                                    gggCGAGAAATGTCATGACAGTGAAGGTGC‑GGTTACTGTCGAAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCttttt                                                     <  2:444742/151‑1 (MQ=255)                                                                                                      gCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttc                                                   >  2:112693/1‑151 (MQ=255)                                                                                                           cAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttcttttt                                              >  1:824061/1‑151 (MQ=255)                                                                                                            aaTTTCAGGACAGGTTAGGTGC‑GTTTACTGTCGAGAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttct                                                  <  1:475696/146‑1 (MQ=255)                                                                                                            aaTGTCATGAAGGTGTGGGTGC‑GTTTCCTGTCGTAAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttctttttc                                             <  2:290494/151‑1 (MQ=255)                                                                                                               gtaaTGACAGTGTGGGGGG‑GTTTACTGTCGTAAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCAc                                           <  1:739069/147‑1 (MQ=255)                                                                                                                   gaacggtgagggggC‑GGTTACGGTCGAAAAAAAAAAAAAAAGCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTTTGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTc                                        <  1:533998/136‑1 (MQ=255)                                                                                                                     aaggtgaAGGTGC‑GGTTCCTGAGGTAAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTc                                        <  1:560443/144‑1 (MQ=255)                                                                                                                      cAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTc                                   >  1:112101/1‑151 (MQ=255)                                                                                                                          gtAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGc                               >  2:579350/1‑151 (MQ=255)                                                                                                                              gggggggTTACTGTCGTAAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACg                                <  1:660167/142‑1 (MQ=255)                                                                                                                              ggggcggtaccggTCGTAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCt                              <  2:302123/137‑1 (MQ=255)                                                                                                                                    ttgaCTGCCGTAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAAc                          <  1:579197/144‑1 (MQ=255)                                                                                                                                                 aaaaaaaaaaaaACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCGCa         <  2:788527/151‑1 (MQ=255)                                                                                                                                                 aaaaCAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCGc          >  2:734195/1‑150 (MQ=255)                                                                                                                                                     cAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCGCAAAAc     >  2:310293/1‑151 (MQ=255)                                                                                                                                                        tAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCGCAAAACCTg  >  1:173348/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                                                       AAAAAGAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGC‑GGTTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCGCAAAACCTG  >  NC_000913/4287569‑4287869

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑