Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,287,710	0	G	A	39.6%	59.7 / 21.3	48	intergenic (‑339/‑54)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
Reads supporting (aligned to +/- strand):  ref base G (24/5);  new base A (0/19);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 7.37e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGCTGTTGAAAAAGAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTC  >  NC_000913/4287560‑4287857                                                                                                                                                       |                                                                                                                                                     atgcTGTTGAAAAAGAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTg                                                                                                                                                      >  1:747045/1‑151 (MQ=255)      gTTGAAAAAGAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGaaa                                                                                                                                                   <  2:692424/149‑1 (MQ=255)          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                                     >  1:235098/1‑151 (MQ=255)                                                                                                                 gAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttctt                                     >  2:678629/1‑151 (MQ=255)                                                                                                                 gAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttctt                                     >  2:184015/1‑151 (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)                                                                                                                                               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)                                                                                                                                                    cGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTc  >  2:723714/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                     ATGCTGTTGAAAAAGAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAAAAACAATAAAAA‑CCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTC  >  NC_000913/4287560‑4287857

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: ‑