Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	435,946	G→A	36.4%	D105N (GAC→AAC)	thiL →	thiamine monophosphate kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	435,946	0	G	A	36.4%	75.0 / 62.7	74	D105N (GAC→AAC)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base G (28/19);  new base A (13/14);  total (41/33)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CCTAAGCGATCTGGCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTGGGTATCCACGGCTTTG  >  NC_000913/435849‑436045                                                                                                  |                                                                                                    ccTAAGCGATCTGGCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGAc                                                                                                   >  2:682898/1‑100 (MQ=255)    aaGCGATCTGGCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAgt                                                                                                >  1:1895034/1‑100 (MQ=255)          tCTGGCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAgtttgttt                                                                                          <  2:169163/100‑1 (MQ=255)            tGGCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGa                                                                                        >  1:1132849/1‑100 (MQ=255)            tGGCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGa                                                                                        >  1:1552572/1‑100 (MQ=255)            tGGCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGa                                                                                        <  2:1945772/100‑1 (MQ=255)            tGGCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGGGGCTTGAGTCCTTCAGCGACAGTTTGTTTGa                                                                                        >  2:839772/1‑100 (MQ=255)             ggCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGAt                                                                                       <  2:1779459/100‑1 (MQ=255)              gCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGTGATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGAtc                                                                                      <  2:478689/100‑1 (MQ=255)              gCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTATCCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGAt                                                                                       <  2:712265/99‑1 (MQ=255)              gCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGAtc                                                                                      <  2:681129/100‑1 (MQ=255)              gCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGAtc                                                                                      >  1:2025159/1‑100 (MQ=255)              gCAGCGATGAGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTCCCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTCTGAtc                                                                                      <  2:2241947/100‑1 (MQ=255)               cAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGAtct                                                                                     >  2:2209342/1‑100 (MQ=255)               cAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGAtc                                                                                      >  2:864977/1‑99 (MQ=255)                 gCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGAtcttc                                                                                   <  2:1132846/100‑1 (MQ=255)                  cGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGAtcttct                                                                                  >  2:414712/1‑100 (MQ=255)                   gATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTtctc                                                                                 >  2:243036/1‑100 (MQ=255)                     tGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCaa                                                                               <  2:869028/100‑1 (MQ=255)                      gggggCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAat                                                                              >  2:284034/1‑100 (MQ=255)                       ggggCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAatt                                                                             >  2:2138390/1‑100 (MQ=255)                        gggCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAatta                                                                            >  2:495982/1‑100 (MQ=255)                         ggCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAattat                                                                           >  1:735389/1‑100 (MQ=255)                         ggCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAattat                                                                           >  1:896997/1‑100 (MQ=255)                         ggCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAattat                                                                           >  2:1899582/1‑100 (MQ=255)                          gCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAattatt                                                                          >  2:1461848/1‑100 (MQ=255)                           ccGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAAttatta                                                                         <  2:1496949/100‑1 (MQ=255)                            ctaTCCGGCCTTGCTGACGCTGTCATTAACCTTACCGGACTTAGACGAATCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTAc                                                                        <  2:2106096/98‑1 (MQ=255)                             gATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACg                                                                       >  1:1211287/1‑100 (MQ=255)                               tCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGat                                                                     >  2:223919/1‑100 (MQ=255)                                ccGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGata                                                                    <  2:735389/100‑1 (MQ=255)                                ccGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGata                                                                    <  2:1554657/100‑1 (MQ=255)                                 cGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGatat                                                                   <  1:1616715/100‑1 (MQ=255)                                 cGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGatat                                                                   >  1:2156503/1‑100 (MQ=255)                                      tGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAAc                                                              >  1:1033086/1‑100 (MQ=255)                                        gCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTc                                                            >  1:889638/1‑100 (MQ=255)                                         cTGACGCTGGCATTAACCTGACCGGACGGAGACTAAGCGTGGCTTGAGTCCTTCAGTGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTc                                                            <  2:2093292/99‑1 (MQ=255)                                            aCGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTg                                                        >  2:821388/1‑100 (MQ=255)                                              gCTGGCATTAACCTTGCCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTggc                                                      <  1:2209357/100‑1 (MQ=255)                                               cTGGCATTAACCTTACCGGATGTAGACTAAGCGTGGCTTTAGTCTTTCAGCAACTGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTggc                                                      <  2:712083/99‑1 (MQ=255)                                               cTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTggcg                                                     <  2:945131/100‑1 (MQ=255)                                                tGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTggcgg                                                    >  2:86527/1‑100 (MQ=255)                                                 ggCATTGACCTTACCGGACGTAAAAGAAGCGTGGCTAGAGAAATTCAGCGACTGTTTGTTTGATCTTCCGACATATTACGATATTCTACTCTTTggc                                                      >  2:844225/1‑97 (MQ=255)                                                 ggCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTggcggc                                                   <  1:976610/100‑1 (MQ=255)                                                  gCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGgcggcg                                                  <  2:1124368/100‑1 (MQ=255)                                                  gCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGgcggcg                                                  >  1:607234/1‑100 (MQ=255)                                                  gCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTCCGATATGCAACTCATTGgcggcg                                                  <  2:448860/100‑1 (MQ=255)                                                    aTTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGAt                                                >  1:373746/1‑100 (MQ=255)                                                    aTTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGGCCTTCAGCGACAGTTTGTTTGATCGTCTCAATTATTACGATATGCAACTCATTGgcggcg                                                  <  2:1210620/98‑1 (MQ=255)                                                        aCCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCa                                            >  1:962937/1‑100 (MQ=255)                                                        aCCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCa                                            >  1:1589271/1‑100 (MQ=255)                                                               cGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTgg                                     <  2:1552561/100‑1 (MQ=255)                                                                ggACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTggg                                    >  2:1907994/1‑100 (MQ=255)                                                                 gACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGc                                   <  1:793425/100‑1 (MQ=255)                                                                  aCGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGcc                                  >  1:1596863/1‑100 (MQ=255)                                                                   cGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGcc                                  >  1:1420487/1‑99 (MQ=255)                                                                     tAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCAtt                               <  1:664618/100‑1 (MQ=255)                                                                       gACGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTAt                             >  2:1923959/1‑100 (MQ=255)                                                                         cGAAGCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCa                           >  1:540724/1‑100 (MQ=255)                                                                          gAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCa                           <  2:108989/99‑1 (MQ=255)                                                                             gCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGa                       >  2:969948/1‑100 (MQ=255)                                                                             gCGTGGCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGa                       <  1:1789512/100‑1 (MQ=255)                                                                               gTGGCTTGAGTCCTTAAGCGACAGTTTGTTTGATGTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGa                       >  2:1840693/1‑98 (MQ=255)                                                                                 ggCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGtt                   >  1:682111/1‑100 (MQ=255)                                                                                 ggCTTGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGtt                   <  2:847984/100‑1 (MQ=255)                                                                                    ttGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTggg                <  1:206619/100‑1 (MQ=255)                                                                                    ttGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTggg                <  1:451301/100‑1 (MQ=255)                                                                                    ttGAGTCCTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTggg                <  1:1092942/100‑1 (MQ=255)                                                                                       aGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTGGGTAt             >  2:1759673/1‑100 (MQ=255)                                                                                          ccTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTGGGTAt             >  2:1352593/1‑97 (MQ=255)                                                                                          ccTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTGGGTATCCa          >  2:1250424/1‑100 (MQ=255)                                                                                          ccTTCAGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTGGGTATCCa          <  1:54972/100‑1 (MQ=255)                                                                                              cAGCAACAGTTTGTTTGATCTTCTCAATTTTTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTGGGTATCCACGGc      <  2:1349400/100‑1 (MQ=255)                                                                                               aGCAACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTGGGTATCCACGGCt     >  2:821719/1‑100 (MQ=255)                                                                                                  gACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTGGGTATCCACGGCTTTg  <  1:816775/100‑1 (MQ=255)                                                                                                  |                                                                                                    CCTAAGCGATCTGGCAGCGATGGGGGCCGATCCGGCCTGGCTGACGCTGGCATTAACCTTACCGGACGTAGACGAAGCGTGGCTTGAGTCCTTCAGCGACAGTTTGTTTGATCTTCTCAATTATTACGATATGCAACTCATTGGCGGCGATACCACGCGTGGGCCATTATCAATGACGTTGGGTATCCACGGCTTTG  >  NC_000913/435849‑436045

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: ‑