Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,361,323	T→A	100%	Q31L (CAG→CTG)	rhmD ←	L‑rhamnonate dehydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,361,323	0	T	A	95.0%	246.1 / 3.3	80	Q31L (CAG→CTG)	rhmD	L‑rhamnonate dehydratase
Reads supporting (aligned to +/- strand):  ref base T (3/1);  new base A (39/37);  total (42/38)
Fisher's exact test for biased strand distribution p-value = 6.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.73e-01

GAACGTTAATGCCAAATGACTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCTGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAGGGTCATGATG  >  NC_000913/2361228‑2361418                                                                                                |                                                                                                gAACGTTAATGCCAAATGACTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTc                                                                                             >  2:1464122/1‑100 (MQ=255)     gTTAATGCCAAATGACTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGa                                                                                         <  1:1631502/100‑1 (MQ=255)      ttAATGCCAAATGACTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGAt                                                                                        <  2:1286164/100‑1 (MQ=255)         aTGCCAAATGACTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAAt                                                                                     <  1:1259208/100‑1 (MQ=255)         aTGCCAAATGACTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAAt                                                                                     >  1:133283/1‑100 (MQ=255)         aTGCCAAATGACTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAAt                                                                                     <  2:730917/100‑1 (MQ=255)             cAAATGACTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCAcc                                                                                 >  1:955607/1‑100 (MQ=255)                 tGACTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCAccgccg                                                                             <  1:1858189/100‑1 (MQ=255)                 tGACTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTAGCCAGTAATTCGCCCCCAGGTCGTGATAATCAcc                                                                                 >  2:1725037/1‑96 (MQ=255)                    cTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCa                                                                          >  1:744363/1‑100 (MQ=255)                      ggCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAgc                                                                        >  2:1317801/1‑100 (MQ=255)                      ggCGTGACTGCTCGTAATCGCGGTATTTACTCACCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCa                                                                          >  2:1122657/1‑98 (MQ=255)                       gCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAgcg                                                                       >  1:1715079/1‑100 (MQ=255)                          tGACTGCTCGT‑ATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCtt                                                                   >  2:1292934/1‑100 (MQ=255)                             cTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCtttt                                                                 <  1:185000/100‑1 (MQ=255)                             cTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCtttt                                                                 <  1:2154841/100‑1 (MQ=255)                              tGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCtttt                                                                 <  1:1124141/99‑1 (MQ=255)                                cTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAGTCACCGCCGCCAGCGCCTTTTTc                                                               >  1:869837/1‑99 (MQ=255)                                cTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTct                                                              >  2:2390172/1‑100 (MQ=255)                                cTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTct                                                              <  2:2292317/100‑1 (MQ=255)                                cTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTct                                                              >  2:2408282/1‑100 (MQ=255)                                cTCGTAATCGCGGTATTTACTCATCGGAGTGGCAATATGATCGTCTATCAAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTct                                                              <  2:2057622/100‑1 (MQ=255)                                 tCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTctg                                                             <  2:1656654/100‑1 (MQ=255)                                 tCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTctg                                                             <  1:1013076/100‑1 (MQ=255)                                 tCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTctg                                                             <  2:2017676/100‑1 (MQ=255)                                  cGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCATGTCGTGATAATCACCGCCGCCAGCGCCTTTTTctgc                                                            <  1:1807024/100‑1 (MQ=255)                                  cGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTctgc                                                            >  1:1165215/1‑100 (MQ=255)                                     aaTCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGt                                                         >  1:1415130/1‑100 (MQ=255)                                     aaTCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGt                                                         >  2:516196/1‑100 (MQ=255)                                      aTCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTc                                                        <  2:2392239/100‑1 (MQ=255)                                        cgcgGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGc                                                      <  1:377749/100‑1 (MQ=255)                                         gcgGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCa                                                     >  1:2321325/1‑100 (MQ=255)                                          cgGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCAc                                                    >  2:2196706/1‑100 (MQ=255)                                           ggTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCAcc                                                   <  1:470274/100‑1 (MQ=255)                                              aTTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGcc                                                <  2:1057518/100‑1 (MQ=255)                                              aTTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGcc                                                >  1:2431294/1‑100 (MQ=255)                                              aTTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGGGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGcc                                                >  1:2431345/1‑100 (MQ=255)                                                 tACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCTGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGt                                             >  1:536496/1‑100 (MQ=255)                                                 tACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAg                                              >  2:1534272/1‑99 (MQ=255)                                                 tACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGt                                             <  2:235289/100‑1 (MQ=255)                                                    tCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTaaa                                          >  2:1660050/1‑100 (MQ=255)                                                      aTCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAAcc                                        <  1:73227/100‑1 (MQ=255)                                                          gggTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGgc                                    <  1:716229/100‑1 (MQ=255)                                                           ggTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGgcg                                   <  2:1819908/100‑1 (MQ=255)                                                           ggTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGgcg                                   >  2:891160/1‑100 (MQ=255)                                                               gCAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGaa                               >  1:820286/1‑100 (MQ=255)                                                                cAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGgcg                                   <  2:272688/95‑1 (MQ=255)                                                                cAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAAc                              <  1:2343395/100‑1 (MQ=255)                                                                cAATATGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAAc                              >  2:1716262/1‑100 (MQ=255)                                                                  atatGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAAcc                             >  1:1394975/1‑99 (MQ=255)                                                                   tatGATCGTCTATCCAGTGATTCGCCCCCAGGTCGGGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTg                           <  2:708274/100‑1 (MQ=255)                                                                     tGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTg                           >  2:670180/1‑98 (MQ=255)                                                                     tGATCGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGtt                         >  2:2419505/1‑100 (MQ=255)                                                                         cGTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCCGTTTAAt                     >  1:319601/1‑100 (MQ=255)                                                                          gTCTATCCAGTGATTCGCCCCCTGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAAtt                    >  2:187276/1‑100 (MQ=255)                                                                          gTCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAAtt                    <  2:2544569/100‑1 (MQ=255)                                                                           tCTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAAttt                   >  1:482405/1‑100 (MQ=255)                                                                            cTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAAtttt                  <  1:2418709/100‑1 (MQ=255)                                                                            cTATCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAAtttt                  <  1:961253/100‑1 (MQ=255)                                                                              aTCCAGTGATTCGCCCCCTGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTg                <  1:187278/100‑1 (MQ=255)                                                                              aTCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTg                <  2:15904/100‑1 (MQ=255)                                                                              aTCCAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTg                >  1:2185003/1‑100 (MQ=255)                                                                               tCCAGTGCTGCGCCCCCAGGTGGTGATAATCACCGCCGCCAGCGCCTGTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAAttttt                 <  2:2191611/98‑1 (MQ=255)                                                                                ccAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGt              <  2:482400/100‑1 (MQ=255)                                                                                ccAGTGATTCGCCCCCAGGTCGTGATAATCACCGCAGGCAGCGCCTTTTGCTGCTGTCGAACCGCAAGAAAACCAGGCGCGAACCAGGCTAAttt                   <  2:1443576/95‑1 (MQ=255)                                                                                 cAGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTa             >  2:2290557/1‑100 (MQ=255)                                                                                  aGTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAg            >  1:1424585/1‑100 (MQ=255)                                                                                  aGTGATTCGCCCCCAGGTCGTGACAATCACCGCAGCCAGCGCCTTTTTCTGTTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTgg               <  2:356407/97‑1 (MQ=255)                                                                                   gTGATTCGCCCCCTGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAgg           >  1:2358121/1‑100 (MQ=255)                                                                                   gTGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAgg           >  1:282954/1‑100 (MQ=255)                                                                                    tGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAggg          <  1:1165621/100‑1 (MQ=255)                                                                                    tGATTCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAggg          <  2:1390158/100‑1 (MQ=255)                                                                                        tCGCCCCCAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAGGGTCat      >  1:1520133/1‑100 (MQ=255)                                                                                         cGCCCCCAGGTCGTGACAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACAGCCAGTAAACCAGGCGCCAACCTGTTTCATTTACGTTAGGGTc        >  2:666317/1‑97 (MQ=255)                                                                                           cccccAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAGGGTCatgat   >  1:2126856/1‑100 (MQ=255)                                                                                           cccccAGGTCGTGATAATCACCGCCGCCAGCGCCCTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAGGGTCatgat   >  2:155592/1‑100 (MQ=255)                                                                                            ccccAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCATCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAGGGTCatga    <  2:1142140/98‑1 (MQ=255)                                                                                            ccccAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAGGGTCatgatg  >  1:173952/1‑100 (MQ=255)                                                                                            ccccAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAGGGTCatgatg  <  1:2290571/100‑1 (MQ=255)                                                                                            ccccAGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAGGGTCatgatg  >  1:735472/1‑100 (MQ=255)                                                                                                |                                                                                                GAACGTTAATGCCAAATGACTGGCGTGACTGCTCGTAATCGCGGTATTTACTCATCGGGGTGGCAATATGATCGTCTATCCAGTGATTCGCCCCCTGGTCGTGATAATCACCGCCGCCAGCGCCTTTTTCTGCTGTCGCACCGCCAGTAAACCAGGCGCGAACCTGTTTAATTTTTGGTAGGGTCATGATG  >  NC_000913/2361228‑2361418

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: ‑