Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,287,719	0	T	A	42.9%	50.3 / 30.0	49	intergenic (‑348/‑45)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
Reads supporting (aligned to +/- strand):  ref base T (19/9);  new base A (0/21);  total (19/30)
Fisher's exact test for biased strand distribution p-value = 4.88e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCGCAAAACCT  >  NC_000913/4287574‑4287868                                                                                                                                                    |                                                                                                                                                      gagGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATaaaaa                                                                                                                                                  <  1:385230/151‑1 (MQ=255)  agGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAAc                                                                                                                                                 >  2:397365/1‑151 (MQ=255)    gAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCg                                                                                                                                               <  1:442487/151‑1 (MQ=255)        aTACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCa                                                                                                                                            <  1:509557/150‑1 (MQ=255)         tACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCAtt                                                                                                                                          >  1:313665/1‑151 (MQ=255)         tACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGG‑TATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTg                                                                                                                                         >  1:535432/1‑151 (MQ=255)             gACTAACTCTAAAGTGGTATTTTACATGCATTTACAATTGATAAAAGACAACATTCACGGTGTGTTTATTTGTTACACATAGGGGCGAGA‑AATGTAAGGACAGTGTAGGGGGGG‑TTACTGTCGTGAAAAAAAATAAAAACCGCCATTGca                                                                                                                                       <  1:549104/150‑1 (MQ=255)                  aCTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATg                                                                                                                                 >  2:608060/1‑151 (MQ=255)                       aaggtgtTATTTTACATGCATTTACAATTGATAAAAAACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGGGG‑TTACTGTGGTAAAAAACAAAAAAAACCGCCATTGCAACAATGGCGCa                                                                                                                            <  2:714674/148‑1 (MQ=255)                             gTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCgg                                                                                                                      >  1:475862/1‑151 (MQ=255)                              tATTTTACATGCACTTACAATTGATAAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGA‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCgg                                                                                                                      <  2:727988/150‑1 (MQ=255)                               aTTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGAt                                                                                                                    >  2:62901/1‑151 (MQ=255)                                   tACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGa                                                                                                                  >  2:180721/1‑149 (MQ=255)                                     ctggcgctttaaattaattAAAAAAACCATTCACGTTGGGGTAATTTGTTACACCGGGGGTCGCGC‑AATGTCACGAAAGTGTAGGTGCGG‑TTACGGTTGTGAAAACTAAAAAAAACCGCCATTTCATCAATGGCGCAATTCGGATGAAGc                                                                                                               <  1:781041/139‑1 (MQ=255)                                      aTGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGccc                                                                                                             >  1:223978/1‑151 (MQ=255)                                       tGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGcccc                                                                                                            >  2:392714/1‑151 (MQ=255)                                           cTTAAAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGT‑TTCCGGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTAt                                                                                                         <  2:453161/150‑1 (MQ=255)                                             tACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGAc                                                                                                      >  2:203948/1‑151 (MQ=255)                                              aaaaTTGATTAAAGACAACATTCACAGTGTGGTTTTTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACa                                                                                                     <  1:67101/149‑1 (MQ=255)                                              aCAATTGATTAAAGACAACATTCACAGTGTGTTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGAc                                                                                                      <  2:51451/150‑1 (MQ=255)                                              aCAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACGGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACa                                                                                                     <  2:765441/151‑1 (MQ=255)                                                aaTTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACa                                                                                                     >  1:69094/1‑149 (MQ=255)                                                     aTTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGGGCGG‑TTACTGTCGTAAAAAAAAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATa                                                                                               <  2:83069/150‑1 (MQ=255)                                                       tAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGACATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATaa                                                                                              >  1:432529/1‑149 (MQ=255)                                                         aagaaaaatttcagtgtgaGGTTTTTTGTCACAGAGGGGGCGGCGC‑AGTGTCAGAAAAGCTTAGGTGGGG‑TTCGTATCGTGAAAACAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAAt                                                                                          <  1:47971/136‑1 (MQ=255)                                                              accaTTCACGGTGTGGTTATTTGTTACCCAGAGGGGCGAGC‑AATGTCATGACAGTGTAGGGGCGG‑TTATTGTCGTAAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAac                                                                                      <  1:710730/148‑1 (MQ=255)                                                              aacaTTCAAAGTGTGGTTATTTTTTACCCATGGGGGCGAGA‑AATTTCATGACAGTGTAGGTGCGT‑TTACTGTCGTGAAAAACAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAacg                                                                                     <  1:18439/151‑1 (MQ=255)                                                                 aTTCACAGTGTGTTTATTTGTTACACATGGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTAAAAAACAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAacgca                                                                                   <  1:735891/150‑1 (MQ=255)                                                                          gtgGTTATTTTTTACACATAGGGGCGAAC‑AATGTCAGGACAGTGTAGGTGCGG‑TTACTGTCGTAAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTAt                                                                           <  1:449165/149‑1 (MQ=255)                                                                          gtgGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCt                                                                         >  2:56857/1‑151 (MQ=255)                                                                            gtttttttGTTACTAAGAGGGGCGAGA‑ATTTTAAGGACAGGTTGGGGGCGG‑TTCCTGTGGAAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTc                                                                       <  1:563492/146‑1 (MQ=255)                                                                              ttttttttaacacAAGGGGGAGACA‑AATGCCAGGACAGTGAGGGGGGGG‑TTACTGCGGAAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCtt                                                                        <  1:467504/139‑1 (MQ=255)                                                                                 ttttttACAC‑TAGGGGCGACCAAAGGTCAGCAAAGTGT‑GGGGCGGTTTATTGTCGGAAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGc                                                                    <  1:359469/149‑1 (MQ=255)                                                                                   tGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTAt                                                                >  2:52309/1‑151 (MQ=255)                                                                                     ttacaaaagggggAGAAC‑AATGTCATAACAGTGGAGGGGGGT‑TTACTGTCGAAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTAtt                                                               <  1:260889/141‑1 (MQ=255)                                                                                               ggggcggaaattGTCATGACATTTTAGGTGGGT‑TAATTGTCGTAAAAAACAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCtt                                                       <  1:87047/138‑1 (MQ=255)                                                                                               gggCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCttttt                                                    >  2:218318/1‑151 (MQ=255)                                                                                                  cGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttct                                                 >  1:640240/1‑151 (MQ=255)                                                                                                      c‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttcttttt                                             >  1:637677/1‑151 (MQ=255)                                                                                                       aattGTCATGAGGGTGTGGGTGGGT‑TTCTTGTCGTAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTtttttcttttt                                             <  2:535396/148‑1 (MQ=255)                                                                                                        aaggccataaaggtggAGGTGCGT‑TTACTGCGGAAAAAAACAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCtttttt                                                   <  1:565856/132‑1 (MQ=255)                                                                                                                    gtgtAGGGGCGG‑TTATGTTCTTAAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGttt                                  <  1:160022/149‑2 (MQ=255)                                                                                                                         ggTGGGT‑TTCCTGTCGTAAAAAAAAAAAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTc                                       <  2:314521/139‑1 (MQ=255)                                                                                                                         ggTGCGT‑TTACTGTCGTAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTg                                     <  2:796810/141‑1 (MQ=255)                                                                                                                             gggtttcttGTCGTAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACa                        <  1:75586/143‑1 (MQ=255)                                                                                                                                  tACTGTCGTAAAAAAAAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACg                    <  2:409725/150‑1 (MQ=255)                                                                                                                                            aaaaaCAAAAAAACCCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGgctg                <  2:783094/144‑1 (MQ=255)                                                                                                                                               aaCAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCGCaa       >  2:1837/1‑150 (MQ=255)                                                                                                                                                   aTAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCGCAAAACCt  >  2:599824/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                                      GAGGAAGATACTGACTAACTCTAAAGTGGTATTTTACATGCACTTACAATTGATTAAAGACAACATTCACAGTGTGGTTATTTGTTACACATAGGGGCGAGC‑AATGTCATGACAGTGTAGGTGCGG‑TTACTGTCGTGAAAAACAATAAAAACCGCCATTGCAACAATGGCGCAATTCGGATGAAGCCCCTATGACAAGGATAAAAATAAACGCACGCCGTATCTTCAGCTTATTGATTCCTTTTTTCTTTTTCACTTCTGTTCACGCTGAACAAACGGCTGCTCCCGCAAAACCT  >  NC_000913/4287574‑4287868

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑