Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,610,369	0	A	T	35.4%	85.6 / 87.3	79	Q69L (CAG→CTG)	hyfH	hydrogenase 4, Fe‑S subunit
Reads supporting (aligned to +/- strand):  ref base A (20/31);  new base T (9/19);  total (29/50)
Fisher's exact test for biased strand distribution p-value = 6.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.17e-01

CCCAGCCAATGTATTGCCTGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACTGACCGTCACCAA  >  NC_000913/2610272‑2610468                                                                                                  |                                                                                                    cccAGCCAATGTATTGCCTGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGc                                                                                                   >  1:1550137/1‑100 (MQ=255)    aGCCAATGTATTGCCTGCGGTGCCTGCGCCTGTGCTTGTCCTGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGctct                                                                                                <  1:141131/100‑1 (MQ=255)    aGCCAATGTATTGCCTGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGctct                                                                                                >  2:1845953/1‑100 (MQ=255)       cAATGTATTGCCTGCGGTGCCTCCGCCTGTGTTTGTCTGGCAAATGCTCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATc                                                                                             <  1:1310356/100‑1 (MQ=255)        aaTGTATTGCCTGTGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCt                                                                                            >  1:1505/1‑100 (MQ=255)         aTGTATTGCCTGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCt                                                                                            <  2:1869890/99‑1 (MQ=255)           gTATTGCCTGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTggg                                                                                         <  2:292956/100‑1 (MQ=255)            tATTGCCTGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTgggg                                                                                        <  1:475415/100‑1 (MQ=255)                gCCTGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGtt                                                                                    >  2:1052/1‑100 (MQ=255)                 ccTGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGCCCACCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTg                                                                                   <  2:1462810/100‑1 (MQ=255)                  cTGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGt                                                                                  >  2:762587/1‑100 (MQ=255)                   tGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTa                                                                                 <  2:60250/100‑1 (MQ=255)                   tGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTa                                                                                 >  1:1003254/1‑100 (MQ=255)                    gCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTAt                                                                                <  2:1003255/100‑1 (MQ=255)                      ggTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTAttt                                                                              >  2:46106/1‑100 (MQ=255)                      ggTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTAttt                                                                              <  2:297068/100‑1 (MQ=255)                       gTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTa                                                                             >  1:1393825/1‑100 (MQ=255)                        tGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTAc                                                                            <  2:1018586/100‑1 (MQ=255)                         gCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACt                                                                           <  2:1805867/100‑1 (MQ=255)                         gCCTGCCCCTGTGCTTGTCCGGCAACTGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTAc                                                                            <  2:272554/99‑1 (MQ=255)                          ccTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTg                                                                          <  1:1032150/100‑1 (MQ=255)                          ccTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTg                                                                          >  2:593637/1‑100 (MQ=255)                           cTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGc                                                                         <  1:540187/100‑1 (MQ=255)                           cTGCGCCTGTCCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACGTGTCAGCTCTATCTGGGGCGTTGTATTTACTGc                                                                         <  1:1279956/100‑1 (MQ=255)                            tGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGATGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCg                                                                        <  1:1536005/100‑1 (MQ=255)                            tGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCg                                                                        <  2:1657314/100‑1 (MQ=255)                             gcgcCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCgg                                                                       <  2:431587/100‑1 (MQ=255)                             gcgcCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCgg                                                                       <  2:1937739/100‑1 (MQ=255)                                   gtgCTTGTCCGGCAAATGCGCTGACTATCCAGACCGTCGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTtg                                                                 <  2:1708318/100‑1 (MQ=255)                                   gtgCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTtg                                                                 >  1:1584566/1‑100 (MQ=255)                                    tgCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTtgt                                                                <  2:1104349/100‑1 (MQ=255)                                      cTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCCAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTga                                                              <  1:1361299/100‑1 (MQ=255)                                      cTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTga                                                              <  2:1393833/100‑1 (MQ=255)                                      cTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTga                                                              <  1:1380750/100‑1 (MQ=255)                                      cTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTga                                                              <  2:753902/100‑1 (MQ=255)                                         gTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTgaaga                                                           <  2:1464557/100‑1 (MQ=255)                                         gTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTgaaga                                                           <  2:1179041/100‑1 (MQ=255)                                         gTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTgaaga                                                           <  2:896142/100‑1 (MQ=255)                                           ccGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTgaagaan                                                         <  1:1505458/100‑2 (MQ=255)                                           ccGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGaagaag                                                         >  2:1121915/1‑100 (MQ=255)                                            cGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAgt                                                        >  1:1254315/1‑100 (MQ=255)                                             ggCAAATGCGCTGACTATCCAGACCGACGTCCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAgtg                                                       <  2:563395/100‑1 (MQ=255)                                             ggCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAgtg                                                       <  1:1683184/100‑1 (MQ=255)                                               cAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGtgtg                                                     <  1:332754/100‑1 (MQ=255)                                                 aaTGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGcc                                                   >  2:801957/1‑100 (MQ=255)                                                 aaTGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGcc                                                   >  2:801956/1‑100 (MQ=255)                                                 aaTGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGcc                                                   <  2:601388/100‑1 (MQ=255)                                                 aaTGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGcc                                                   <  1:955127/100‑1 (MQ=255)                                                 aaTGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGc                                                    <  2:265460/99‑1 (MQ=255)                                                    gcgcTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGa                                                >  1:1580806/1‑100 (MQ=255)                                                          aCTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCagag                                          <  1:191072/100‑1 (MQ=255)                                                           cTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGc                                         <  1:1194721/100‑1 (MQ=255)                                                            tATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGcc                                        >  2:783611/1‑100 (MQ=255)                                                             aTCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGATGTTGTGAAGAAGTGTGCCCGACCAGAGCCa                                       >  2:1453804/1‑100 (MQ=255)                                                              tCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCAt                                      >  1:195786/1‑100 (MQ=255)                                                                   aCCGACGACCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGc                                 >  1:137170/1‑100 (MQ=255)                                                                    ccGACGTCCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAg                                  <  1:155949/98‑1 (MQ=255)                                                                      gacgacCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTa                              <  1:239940/100‑1 (MQ=255)                                                                       acgacCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTAc                             >  2:1340458/1‑100 (MQ=255)                                                                        cgacCAGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTAcc                            <  2:1551207/100‑1 (MQ=255)                                                                          acCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCaa                          >  1:740334/1‑100 (MQ=255)                                                                           ccAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAAt                         <  2:1177925/100‑1 (MQ=255)                                                                            cAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATa                        <  1:1399888/100‑1 (MQ=255)                                                                             aGCAAAATTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATaa                       <  2:1572561/100‑1 (MQ=255)                                                                                aaaaTTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACtt                    <  2:1254319/100‑1 (MQ=255)                                                                                aaaaTTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACtt                    >  2:1256301/1‑100 (MQ=255)                                                                                 aaaTTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGAAGTTGTGAAGAAGTGTGGCCGACCAGAGCCATCCAGCTTCACAATCACttt                   >  1:1870022/1‑100 (MQ=255)                                                                                   aTTCGCGCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGa                 <  2:137171/100‑1 (MQ=255)                                                                                      cgcgCACCTGGCTGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACt              >  1:1679145/1‑100 (MQ=255)                                                                                      cgcgCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACt              >  1:307764/1‑100 (MQ=255)                                                                                       gcgcACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGAAGTTGTGAAGAAGTATGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACTg             >  2:1600341/1‑100 (MQ=255)                                                                                        cgcACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACTGa            >  2:1152402/1‑100 (MQ=255)                                                                                          nacatGGCAAGTCGATCTGAGACGTTGTATTTACAGAGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACGGAcc          >  1:469498/5‑100 (MQ=255)                                                                                           aCCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACTGACCg         <  2:1860775/100‑1 (MQ=255)                                                                                            ccTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACTGACCGt        >  2:1666838/1‑100 (MQ=255)                                                                                               ggCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACTGACCGTCAc     <  1:1256297/100‑1 (MQ=255)                                                                                                gCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACTGACCGTCAcc    <  2:1291901/100‑1 (MQ=255)                                                                                                 cAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACTGACCGTCACCa   <  1:1642455/100‑1 (MQ=255)                                                                                                 cAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCGTACCAATAACTTTGAACTGACCGTCACCa   <  2:1505/100‑1 (MQ=255)                                                                                                  aGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACTGACCGTCACCaa  <  1:1657033/100‑1 (MQ=255)                                                                                                  |                                                                                                    CCCAGCCAATGTATTGCCTGCGGTGCCTGCGCCTGTGCTTGTCCGGCAAATGCGCTGACTATCCAGACCGACGACCAGCAAAATTCGCGCACCTGGCAGCTCTATCTGGGGCGTTGTATTTACTGCGGACGTTGTGAAGAAGTGTGCCCGACCAGAGCCATCCAGCTTACCAATAACTTTGAACTGACCGTCACCAA  >  NC_000913/2610272‑2610468

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑