Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	1,631,843	T→C	A40A (GCA→GCG)	SAUSA300_RS08065 ←	integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	1,631,843	0	T	C	100.0%	210.3 / NA	80	A40A (GCA→GCG)	SAUSA300_RS08065	integrase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (5/75);  total (5/75)

CATCTGAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACTGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACGTGTTTTATAGTCTAAT  >  NC_007793/1631746‑1631936                                                                                                  |                                                                                              cATCTGAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGc                                                                                             <  1:5319059/100‑1 (MQ=255)     tGAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcatct                                                                                         <  1:3026858/100‑2 (MQ=255)     tGAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcatag                                                                                         <  1:2907754/100‑3 (MQ=255)      gAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcatcat                                                                                        <  1:4320320/100‑1 (MQ=255)      gAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcatcat                                                                                        <  1:1370424/100‑1 (MQ=255)      gAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcatcat                                                                                        <  1:1417742/100‑1 (MQ=255)      gAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcatcag                                                                                        <  1:3555163/100‑2 (MQ=255)          tactacGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCAtcatcagc                                                                                    <  1:3252548/100‑3 (MQ=255)          tactacGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACg                                                                                    <  1:1204676/100‑1 (MQ=255)          tactacGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACg                                                                                    <  1:1508741/100‑1 (MQ=255)          tactacGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACg                                                                                    <  1:6289871/100‑1 (MQ=255)          tactacGCGATTTTATAGCATCTTCCACAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACg                                                                                    <  1:3954005/100‑1 (MQ=255)           actacGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAGACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACgg                                                                                   <  1:6168258/100‑2 (MQ=255)             tacGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGAcc                                                                                 <  1:3999024/100‑1 (MQ=255)              tcgcgATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCt                                                                                <  1:2105747/99‑1 (MQ=255)              gcgcgATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCt                                                                                <  1:224430/99‑1 (MQ=255)              acGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCt                                                                                <  1:6370139/100‑1 (MQ=255)              acGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCt                                                                                <  1:1651789/100‑1 (MQ=255)               cgcgATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTa                                                                               <  1:46408/100‑1 (MQ=255)               cgcgATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTa                                                                               <  1:6404657/100‑1 (MQ=255)               cgcgATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTa                                                                               <  1:4349562/100‑1 (MQ=255)               cgcgATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTa                                                                               <  1:1165481/100‑1 (MQ=255)                gcgATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTag                                                                              <  1:1827460/100‑2 (MQ=255)                gcgATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTaa                                                                              <  1:6041941/100‑1 (MQ=255)                gcgATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTaa                                                                              <  1:3993648/100‑1 (MQ=255)                 cgATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTaaa                                                                             <  1:193922/100‑1 (MQ=255)                      ttATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCtt                                                                        <  1:3124418/100‑1 (MQ=255)                      ttATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCtt                                                                        <  1:1798917/100‑1 (MQ=255)                      ttATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCtt                                                                        <  1:5782611/100‑1 (MQ=255)                      ttATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCtt                                                                        <  1:561647/100‑1 (MQ=255)                      ttATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCtt                                                                        <  1:5436387/100‑1 (MQ=255)                      tcttccgaTCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCtt                                                                        <  1:6508233/93‑1 (MQ=255)                       tataGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTa                                                                       <  1:1617822/100‑1 (MQ=255)                        ttccgaTCTTCCTCGGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAg                                                                      <  1:4920354/95‑1 (MQ=255)                        ataGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAg                                                                      <  1:4521344/100‑1 (MQ=255)                         tccgaTCTTCCTTAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTaca                                                                     <  1:1404938/96‑3 (MQ=255)                              tccgatcttgCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGTCCTAAAATCTTAGAAATCt                                                                <  1:6649704/91‑1 (MQ=255)                               cTTCCTTGGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTg                                                               <  1:4919473/100‑1 (MQ=255)                               cTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTg                                                               <  1:5863402/100‑1 (MQ=255)                                ctCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGaagatcgg                                                              >  1:1322692/2‑94 (MQ=255)                                 tCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGag                                                             <  1:1811654/100‑2 (MQ=255)                                     cAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAatgat                                                         >  1:791075/1‑100 (MQ=255)                                          aataaAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTa                                                    >  1:4883286/1‑100 (MQ=255)                                                ggATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACcat                                              <  1:2093597/100‑1 (MQ=255)                                                             cATCAACAGAACGCTTATTTACTTCTCTATAAAGAGCCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACtt                                 <  1:4447633/100‑1 (MQ=255)                                                             cATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACtt                                 >  1:4238670/1‑100 (MQ=255)                                                              aTCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAAGCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAGTACttt                                <  1:5644497/100‑1 (MQ=255)                                                               tCAACGGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTg                               >  1:7669/1‑100 (MQ=255)                                                               tCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGTCCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTg                               <  1:4285630/100‑1 (MQ=255)                                                                cAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTgt                              <  1:1482733/100‑2 (MQ=255)                                                                cAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGc                              <  1:4387568/100‑1 (MQ=255)                                                                cAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGc                              <  1:6199198/100‑1 (MQ=255)                                                                 aaCAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCGCGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCg                             <  1:2849284/100‑1 (MQ=255)                                                                 aaCAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCg                             <  1:2811617/100‑1 (MQ=255)                                                                 aaCAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCg                             <  1:6298579/100‑1 (MQ=255)                                                                 aaCAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTGAAATACTTTGCg                             <  1:269315/100‑1 (MQ=255)                                                                 aaCAGAACGCTTATCTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCg                             <  1:4874614/100‑1 (MQ=255)                                                                   cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                           <  1:898485/100‑1 (MQ=255)                                                                   cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                           <  1:2846293/100‑1 (MQ=255)                                                                   cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                           <  1:6331150/100‑1 (MQ=255)                                                                   cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                           <  1:3261644/100‑1 (MQ=255)                                                                   cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                           <  1:3386228/100‑1 (MQ=255)                                                                   cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                           <  1:3512351/100‑1 (MQ=255)                                                                   cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                           <  1:5723933/100‑1 (MQ=255)                                                                   cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                           <  1:4531462/100‑1 (MQ=255)                                                                   cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                           <  1:446274/100‑1 (MQ=255)                                                                   cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                           <  1:3799547/100‑1 (MQ=255)                                                                   cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                           <  1:3625732/100‑1 (MQ=255)                                                                    aGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCCCGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACGTTGCGATa                          <  1:565467/100‑1 (MQ=255)                                                                     gAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGagat                         <  1:620377/100‑4 (MQ=255)                                                                       aCGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCt                       <  1:3971571/100‑1 (MQ=255)                                                                       aCGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCt                       <  1:1146521/100‑1 (MQ=255)                                                                       aCGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCt                       <  1:533963/100‑1 (MQ=255)                                                                       aCGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCt                       <  1:5721419/100‑1 (MQ=255)                                                                         gCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAg                     <  1:6506997/100‑1 (MQ=255)                                                                           ttATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAggt                   <  1:648786/100‑3 (MQ=255)                                                                               ttACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACgtgt               <  1:3285759/100‑1 (MQ=255)                                                                               ttACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACgtag               <  1:4680257/100‑3 (MQ=255)                                                                                tACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACGTGtt              <  1:1506558/100‑1 (MQ=255)                                                                                            aaGAACCGCATCATCACGACCTAAAATCTTAGAAAGCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACGTGTTTTATAATCTAAt  <  1:3828313/100‑1 (MQ=255)                                                                                                  |                                                                                              CATCTGAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACTGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACGTGTTTTATAGTCTAAT  >  NC_007793/1631746‑1631936

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑