Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,033,233	0	A	T	70.0%	117.6 / 72.6	80	P365P (CCA→CCT)	hyaA	hydrogenase 1, small subunit
Reads supporting (aligned to +/- strand):  ref base A (11/13);  new base T (26/30);  total (37/43)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.75e-01

GGCGTGGTGGCAGCGGCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTCGACCCGATTACGC  >  NC_000913/1033135‑1033329                                                                                                   |                                                                                                 ggCGTGGTGGCAGCGGCTGTTGGTGTGCACGCATTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAg                                                                                                 >  1:1285749/1‑100 (MQ=255)       gtggCAGCGGCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATg                                                                                           >  2:912960/1‑100 (MQ=255)         ggCAGCGGCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAg                                                                                         <  2:806655/100‑1 (MQ=255)          gCAGCGGCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAgg                                                                                        <  2:860155/100‑1 (MQ=255)          gCAGCGGCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAgg                                                                                        <  2:1655621/100‑1 (MQ=255)          gCAGCGGCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAgg                                                                                        <  1:1480777/100‑1 (MQ=255)           cAGCGGCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGa                                                                                       >  2:220561/1‑100 (MQ=255)             gCGGCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATa                                                                                     >  2:1942311/1‑100 (MQ=255)              cGGCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATaa                                                                                    <  1:985072/100‑1 (MQ=255)               ggCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATaaa                                                                                   >  2:1550283/1‑100 (MQ=255)                gCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGa                                                                                       <  1:511814/95‑1 (MQ=255)                gCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAAc                                                                                  >  2:219151/1‑100 (MQ=255)                gCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAAc                                                                                  <  2:1243709/100‑1 (MQ=255)                gCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAAc                                                                                  <  1:744852/100‑1 (MQ=255)                gCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCACACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATa                                                                                     <  1:111454/97‑1 (MQ=255)                 cTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACa                                                                                 <  1:1437219/100‑1 (MQ=255)                   gTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAgg                                                                               >  1:707954/1‑100 (MQ=255)                   gTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAgg                                                                               <  2:55285/100‑1 (MQ=255)                      ggTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCAt                                                                            <  1:1162282/100‑1 (MQ=255)                      ggTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCAt                                                                            <  1:446548/100‑1 (MQ=255)                       gtgtGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATg                                                                           <  1:198860/100‑1 (MQ=255)                       atctgCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATg                                                                           <  1:1538738/97‑1 (MQ=255)                         gtgCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAg                                                                         <  2:64225/100‑1 (MQ=255)                          tgCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGc                                                                        <  1:119873/100‑1 (MQ=255)                           gCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCa                                                                       >  1:1482061/1‑100 (MQ=255)                           gCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAgat                                                                       >  2:1538746/1‑98 (MQ=255)                            cACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCAc                                                                      >  1:960331/1‑100 (MQ=255)                               gCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCa                                                                   <  1:584670/100‑1 (MQ=255)                                 aGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAg                                                                  >  1:1684280/1‑99 (MQ=255)                                   tCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTAc                                                               <  2:1713568/100‑1 (MQ=255)                                   tCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTAc                                                               <  2:602707/100‑1 (MQ=255)                                    cGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACg                                                              >  1:1554343/1‑100 (MQ=255)                                      ccAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGaa                                                            >  2:1806257/1‑100 (MQ=255)                                      ccAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGaa                                                            >  1:976384/1‑100 (MQ=255)                                      ccAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGaa                                                            <  2:817228/100‑1 (MQ=255)                                       aaGCGCCGTTGACAAGCGAAGACGTCCTAACCAGCAACCTACACAACCCGAACATCAGCCTGGCAATGAGTATAAACAGGCATGAGCACTCTGTACgtt                                                            <  1:647140/98‑3 (MQ=255)                                        aGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAAc                                                          <  1:250686/100‑1 (MQ=255)                                          cgcCGTTGACCAGCGCAGACGTCATAGCCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTc                                                        >  2:1184391/1‑100 (MQ=255)                                             cGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAgg                                                     <  1:763452/100‑1 (MQ=255)                                              gTTGACCAGCGCAGCCGTCATAACCAGCAACCTACAGAAACCGAACATCCGCCAGGCAATGTGGATAAACAGTCAAGAGCACTCATTACGAAACTCAg                                                      >  1:1565507/1‑98 (MQ=255)                                                 gACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATa                                                 >  1:468311/1‑100 (MQ=255)                                                 gACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATa                                                 >  2:852556/1‑100 (MQ=255)                                                  aCCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATac                                                >  2:1088956/1‑100 (MQ=255)                                                     ngcgcAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACAcc                                             >  2:846319/2‑100 (MQ=255)                                                       cgcAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCAt                                           <  1:1108599/100‑1 (MQ=255)                                                        gcAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCAtn                                          <  2:523158/100‑2 (MQ=255)                                                        gcAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATc                                          <  1:1682804/100‑1 (MQ=255)                                                        gcAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATc                                          >  2:1943953/1‑100 (MQ=255)                                                           gACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCaat                                       <  1:1884351/100‑1 (MQ=255)                                                            aCGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCaata                                      <  1:1623136/100‑1 (MQ=255)                                                             cGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCaataa                                     <  2:1292686/100‑1 (MQ=255)                                                             cGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCaataa                                     >  1:1419790/1‑100 (MQ=255)                                                               tCATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATg                                   >  1:197034/1‑100 (MQ=255)                                                                cATAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCAATCAGTACGAAACTCAGGGATACAACATCAATAATGc                                  >  1:1628302/1‑100 (MQ=255)                                                                cATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGc                                  <  1:1121484/100‑1 (MQ=255)                                                                 aTAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGcc                                 >  2:1015771/1‑100 (MQ=255)                                                                 aTAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGcc                                 >  2:649307/1‑100 (MQ=255)                                                                 aTAACCAGCAACCTACAGAAACAGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATg                                   >  1:140778/1‑98 (MQ=255)                                                                  tAACCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCg                                >  1:632789/1‑100 (MQ=255)                                                                    aCCAGCAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGa                              <  1:912959/100‑1 (MQ=255)                                                                         cAACCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGAcgccg                         >  2:286255/1‑100 (MQ=255)                                                                           aCCTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACgccgcc                       >  2:706461/1‑100 (MQ=255)                                                                            ccTACAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCt                      <  1:1403444/100‑1 (MQ=255)                                                                             cTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCt                      <  1:1441097/99‑1 (MQ=255)                                                                               aCAGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCtggt                   <  2:1750910/100‑1 (MQ=255)                                                                                cAGAAACCGAACATCAGCCATGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCtggtg                  >  1:1193168/1‑100 (MQ=255)                                                                                cAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCtggtg                  >  2:629315/1‑100 (MQ=255)                                                                                cAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCtggtg                  <  1:1783817/100‑1 (MQ=255)                                                                                 aGAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCAGGACGCCGCCtggtgg                 >  2:1891208/1‑100 (MQ=255)                                                                                  gAAACCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTggtggt                <  2:732665/100‑1 (MQ=255)                                                                                   aaaCCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTc               <  1:229404/100‑1 (MQ=255)                                                                                   aaaCCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTc               <  2:734843/100‑1 (MQ=255)                                                                                   aaaCCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTc               <  1:1741914/100‑1 (MQ=255)                                                                                    aaCCGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTCg              >  1:1251622/1‑100 (MQ=255)                                                                                       cGAACATCAGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTCGAcc           >  2:142230/1‑100 (MQ=255)                                                                                           cATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTCGACCCGAt       <  2:811373/100‑1 (MQ=255)                                                                                               aGCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTCGACCCGATTAcg   >  2:554327/1‑100 (MQ=255)                                                                                                gCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTCGACCCGATTAcgc  <  1:1806246/100‑1 (MQ=255)                                                                                                gCCTGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTCGACCCGATTAcgc  >  2:54648/1‑100 (MQ=255)                                                                                                gCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTCGACCCGATTAcgc  <  2:1601728/100‑1 (MQ=255)                                                                                                   |                                                                                                 GGCGTGGTGGCAGCGGCTGTTGGTGTGCACGCAGTCGCCAGCGCCGTTGACCAGCGCAGACGTCATAACCAGCAACCTACAGAAACCGAACATCAGCCAGGCAATGAGGATAAACAGGCATGAGCACTCAGTACGAAACTCAGGGATACACCATCAATAATGCCGGACGCCGCCTGGTGGTCGACCCGATTACGC  >  NC_000913/1033135‑1033329

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑