Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	954,388	0	C	T	56.2%	‑3.6 / 23.3	33	A27T (GCA→ACA)	focA	formate channel
Reads supporting (aligned to +/- strand):  ref base C (3/11);  new base T (0/18);  total (3/30)
Fisher's exact test for biased strand distribution p-value = 7.34e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.39e-01

AGAAGCAAATGCCGCCAACCAGTTTTGCCATGCCGAAGGGCATTGTGCCTGTGCCAGTGGTTGCTGTGATATAGAAGACGAATGCGATT‑GAGATGAAAACACCGGCGG‑TAAT‑CGCCAGATAGAAAGTCTTAAGCGGATGTTTCGTTGCTTTATAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGAT  >  NC_000913/954241‑954531                                                                                                                                                       |                                                                                                                                                agaAGCAAATGCCGCCAACCAGTTTTGCCATGCCGAAGGGCATTGTGCCTGTGCCAGTGGTTGCTGTGATATAGAAGACGAATGCGATT‑GAGATGAAAACACCGGCGG‑TAAT‑CGCCAGATAGAAAGTCTTAAGCGGATGTTTCGTTGCttt                                                                                                                                              <  1:669226/151‑1 (MQ=255)   aaGCAAATGCCGCCAACCAGTTTTGCCATGCCGAAGGGCATTGTGCCTGTGCCAGTGGTTGCTGTGATATAGAAGACGAATGCGATT‑GAGATGAAAACACCGGCGG‑TAAT‑CGCCAGATAGAAAGTCTTAAGCGGATGTTTCGTTGCTTtat                                                                                                                                            <  2:43018/151‑1 (MQ=255)      cAAATGCCGCCAACCAGTTTTGCCATGCCGAAGGGCATTGTGCCTGTGCCAGTGGTTGCTGTGATATAGAAGACGAATGCGATT‑GAGATGAAAACACCGGCGG‑TAAT‑CGCCAGATAGAAAGTCTTAAGCGGATGTTTCGTTGCttt                                                                                                                                              >  2:345559/1‑146 (MQ=255)                  aCCAGTTTTGCCATGCCGAAGGGCATTGTGCCTGTGCCAGTGGTTGCTGTGATATAGAAGACGAATGCGATT‑GAGATGAAACCCCCGGCGG‑TAAT‑CGCCAGATAGAAAGTCTTAAGCGGATGTTTCGTTGCTTTATAGACACCCGCCTCtt                                                                                                                             <  2:388716/151‑1 (MQ=255)                       tttgcccATGCGGAAGGGTTTGGTGCCTGTGCCGGGGGTTGCTGTGATATAGAAGACAAAGGCGATT‑GAGATGAAAACCCGGGCGG‑TAAT‑CGCCAGATAGAAAGTCTTAAGCGGATGTTTCGTTGTTTTATAGCCACCCGCCTCTTCGGc                                                                                                                         <  2:157987/145‑1 (MQ=255)                          tGCCATGCAGAAGTACATTGTGCATGTACCAGTGGTTGTTGTAATATAGAAGAC‑AAAGAAATTGGAGA‑AAAAACCCCGGTGGATAAT‑CGCCGGAAAGAAAGTCTTAGGGGGATGTTTCGTTGTTTTATACACACCCGCCTCTTCGGCCa                                                                                                                       <  2:442839/149‑1 (MQ=255)                            ccATGCCGAAGGGCATTGTGCCTGTGCCAGTGTTTGTTGTGATAAAAAAGACGAAGGCGATT‑GAGATGAAACCCCCGGCGG‑TAAT‑CGCCAGATAGAAAGTCTTAAGCGGATGTTTCTTTGCTTTATAGACCCCCGCCTCTTCGGCCACtt                                                                                                                    <  1:366683/150‑1 (MQ=255)                              aTGCCGAAGGGCATTGTGCCTGTGCCAGTGGTTGCTGTGATATAGAAGACGAATGCGATT‑GAGATGAAAACACCGGCGG‑TAAT‑CGCCAGATAGAAAGTCTTAAGCGGATGTTTCGTTGCTTTATAGACACCCGCCTCTTCGGCCACTTTgg                                                                                                                 >  1:665327/1‑151 (MQ=255)                                           ttGTGCCTGTGCCAGTGGTTGCTGTGATATAGAAGACGAATGCGATT‑GAGATAAAAACCCCGGCGG‑TAAT‑CGCCAGATAGAAAGTCTTAAGCGGTTGTTTCGTTGCTTTATAGACACCCGCCTCTTCGGCCACTTTGGCCATTgcagca                                                                                                      <  1:405795/149‑1 (MQ=255)                                             gtgcttggcccggTGGTTGTTGGAATATAGAAGAGAAGGGCGTTT‑GAGAGAAAACCCCCGGCGG‑TAAT‑CGCCAGATAAAAATTCTAAGGCGGATGTTTCGTTGCTTAAAAGACCCCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAgg                                                                                                    <  2:626070/137‑1 (MQ=255)                                              tgcctgtgccAGTGGTTGCTGTGATATAGAAAACGAATGCGATT‑GAAATAAAAACCCCGGCGT‑TAAT‑CCCAAGATAAAAATTCTTAAGCGGTTGTTTGGTGGTTTTATAGACGCCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAgg                                                                                                    <  1:631561/148‑1 (MQ=255)                                                  tgtgccTGTGTTTGTTGTGATTTAGAAGACGAGTTCGTTT‑GATATAAAACCCCCGGCGG‑TAAT‑CCCAAGAAAAAAAGTCTTAAGCGGATGTTTGTTTTTTTTAAAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAgg                                                                                                    <  1:739874/144‑1 (MQ=255)                                                             ttGCTGTGATATAGAAGACGAATGCGTTT‑GAGATAAAAACACCGGCGG‑TAAT‑CGCCAGATAAAAAGTCTTAAGCGGATGTTTCGTTGTTTTATACACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCaa                                                                                      <  1:663821/147‑1 (MQ=255)                                                                  gtgATATAGAAGAGGAATGGGATT‑GAGATGAAAACCCCGGCGG‑TAAT‑CCCCAGATAGAAAGTCTTAAGCGGTTTTTTCGTTGTTTTATAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGtt                                                                               <  1:395143/149‑1 (MQ=255)                                                                     atatAAAAGACAAATGCGATT‑GAAATAAAAACCCCGGGGG‑TAAC‑CGCCAGAAAAAAAGTCTTAAGCGGATGTTTCTTTGTTTTAAAGACCCCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCa                                                                           <  1:169916/150‑1 (MQ=255)                                                                      tataGAAGACAAATGCGTTT‑GAGATGAAAACCCCGGCGT‑AAAG‑CGCAAAATAAAAATTCTAAAGCGGTTGTTTCGTTGCTTAAAAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAg                                                                          <  2:541396/150‑1 (MQ=255)                                                                           aagaCAAATGCAATT‑GAGAAG‑AAACCCCGGGGG‑GAATCCCCCAGATAAAAAGTTTTACGGGGTTTTTCGGTTGTTTTAAAAACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTca                                                                    <  2:378352/151‑1 (MQ=255)                                                                               cGAATGCGATT‑GAGATGAAAACACCGGCGG‑TAAT‑CGCCAGATAGAAAGGCTTAAGCGGGTGTTTCGTTGCTTTATAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCacac                                                                 >  2:521472/1‑150 (MQ=255)                                                                                 aaTGCGATT‑GAGATAAAAACCCCGGCGG‑TAAC‑CGCCAGATAGAAAGTCTTAAGCGGATGTTTCGTTGCTTTATAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACt                                                                <  1:343751/149‑1 (MQ=255)                                                                                    gCGATT‑GAGATAAAACCCCGGGCGG‑TAAC‑CGCCAGATAGAAAGTCTAAAGCGGATGTTTGGTTGTTTTATAAACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAActc                                                           <  2:245655/151‑1 (MQ=255)                                                                                      gATT‑GAGATAAAAACCCCGGCGG‑AAAT‑CGCCAGATAGAAAGTCTTAGGCGGATTTTTCTTTGTTTTAAAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAActct                                                          <  1:426679/150‑1 (MQ=255)                                                                                                 aaaaCCCCGGCGG‑AAAC‑CGCCAGATAGAAAGTCTAAAGGGGTTGTTTCGTTGTTTTAAAGCCACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTttat                                                  <  2:280478/148‑1 (MQ=255)                                                                                                  aaccacGGGCGG‑TAAT‑CGCCAAATAGAAATTCTAAAGGGAATTTTTGTTTGTTTAAAAAACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAg                                              <  2:635518/148‑1 (MQ=255)                                                                                                            gg‑TAAT‑CGCCAGAAAGAAAGTTTTAAGCGGTTGTTTCGTTGTTTTATAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGcgacg                                     <  2:742669/150‑1 (MQ=255)                                                                                                                aaT‑CGCCAGATAGAAAGTCTTAAGCGGATGTTTCGTTGCTTTATAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGAt                                 <  1:44217/151‑1 (MQ=255)                                                                                                                  atcccgaGATAGAAAATTTAACGCGGTTGTTTGGTTGATTGATATACTACCGCCTCTTCGGCCGCTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCGCTTTATTAAGTCGGcgacg                                     <  1:612108/140‑1 (MQ=255)                                                                                                                            aGAAAGTCTTAAGGGGATGTTTCGTTGCTTTATAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAg                       <  1:606222/150‑1 (MQ=255)                                                                                                                               aattttaaaGCGGATGTTTCGTTGTTTTATAGACCCCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCAtt                   <  1:503197/144‑1 (MQ=255)                                                                                                                                      aaGCGGTTTTTTCGTTGTTTTATAGACCCCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGa              <  1:730611/149‑1 (MQ=255)                                                                                                                                      aaGCGGATGTTTCGTTGCTTTAAAGACCCCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGAt             <  2:476620/150‑1 (MQ=255)                                                                                                                                       aggggtggTTTGGTTGTTTTATAGCCACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGAAGAGATACTAACAAAGCATtat                 <  1:521496/138‑1 (MQ=255)                                                                                                                                          ggttGTTTCGTTGTTTTATAGACCCCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATgaga         <  1:284867/147‑1 (MQ=255)                                                                                                                                                 tCGTTGTTTTATAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGat  <  2:332712/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                AGAAGCAAATGCCGCCAACCAGTTTTGCCATGCCGAAGGGCATTGTGCCTGTGCCAGTGGTTGCTGTGATATAGAAGACGAATGCGATT‑GAGATGAAAACACCGGCGG‑TAAT‑CGCCAGATAGAAAGTCTTAAGCGGATGTTTCGTTGCTTTATAGACACCCGCCTCTTCGGCCACTTTGGCCATTGCAGCAGGAAGTAAAAGATCAAAAGGGTTGTCAGCTTTCACACTAACTCTCTCTTTATTAAGTCGGCGACGAGATACTAACAAAGCATTATAGATGAGAAATTGAT  >  NC_000913/954241‑954531

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑