Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	1,631,061	C→T	A79T (GCA→ACA)	SAUSA300_RS08060 ←	integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	1,631,061	0	C	T	100.0%	225.8 / NA	79	A79T (GCA→ACA)	SAUSA300_RS08060	integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (5/74);  total (5/74)

ACACAGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGCATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTT  >  NC_007793/1630964‑1631152                                                                                                  |                                                                                            acacaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAt                                                                                           <  1:3618854/100‑1 (MQ=255)  tcttgTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAtt                                                                                          <  1:3342166/96‑1 (MQ=255)  ctcaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAtt                                                                                          <  1:1439610/98‑1 (MQ=255)  cacaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAtt                                                                                          <  1:2523246/100‑1 (MQ=255)  cacaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAtt                                                                                          <  1:824429/100‑1 (MQ=255)  cacaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAtt                                                                                          <  1:3821749/100‑1 (MQ=255)  cacaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAtt                                                                                          <  1:1466649/100‑1 (MQ=255)  cacaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAtt                                                                                          <  1:1419166/100‑1 (MQ=255)  cacaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAtg                                                                                          <  1:2812590/100‑2 (MQ=255)   acaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTa                                                                                         <  1:2969032/100‑1 (MQ=255)   acaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTa                                                                                         <  1:5608334/100‑1 (MQ=255)   acaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTa                                                                                         <  1:2657246/100‑1 (MQ=255)      gTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAAtt                                                                                      >  1:4903656/1‑100 (MQ=255)          tttAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGtt                                                                                  <  1:1962439/100‑1 (MQ=255)          tttAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGtg                                                                                  <  1:3958702/100‑2 (MQ=255)          tttAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGta                                                                                  <  1:5570649/100‑2 (MQ=255)           ttAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGttt                                                                                 <  1:1146795/100‑1 (MQ=255)           ttAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGttt                                                                                 <  1:586663/100‑1 (MQ=255)            tAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTa                                                                                <  1:5038728/100‑1 (MQ=255)            tAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTa                                                                                <  1:523011/100‑1 (MQ=255)              atatAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAAc                                                                              <  1:2484779/100‑1 (MQ=255)              atatAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCAATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAAc                                                                              <  1:5372806/100‑1 (MQ=255)                   ggTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCtt                                                                         <  1:3393534/100‑1 (MQ=255)                    tttCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTc                                                                        >  1:2062567/2‑100 (MQ=255)                     ttCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCa                                                                       <  1:2001200/100‑1 (MQ=255)                       cacaATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATc                                                                     >  1:2940766/1‑100 (MQ=255)                        acaATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCt                                                                    <  1:1268289/100‑1 (MQ=255)                         caATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTa                                                                   <  1:5530337/100‑1 (MQ=255)                         caATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTa                                                                   <  1:150787/100‑1 (MQ=255)                                 cttccgatcttGGTGCTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACttt                                                           <  1:2344094/90‑1 (MQ=255)                                  gtgCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACtttt                                                          <  1:5041581/100‑1 (MQ=255)                                       atcttGGTGCTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGtt                                                     <  1:918081/96‑1 (MQ=255)                                         ttccgatcTTTCGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTgtgtgct                                                   <  1:3895263/93‑4 (MQ=255)                                         tctGGTATTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCTTGTATTAATTTTTTTAACAGCTTCATCTAATGACTTTTGTGttcg                                                   <  1:823862/98‑3 (MQ=255)                                         tctGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTtat                                                   <  1:5164676/98‑1 (MQ=255)                                          aTGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTtata                                                  <  1:1244216/100‑1 (MQ=255)                                           tGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTatat                                                 >  1:5465362/1‑100 (MQ=255)                                                cTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCa                                            <  1:1655417/100‑1 (MQ=255)                                                 tttAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCaa                                           <  1:5078843/100‑1 (MQ=255)                                                            ccgatctcgtttATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCt                                <  1:1216921/91‑1 (MQ=255)                                                             tCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCtt                               <  1:5468175/100‑1 (MQ=255)                                                             tCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCtt                               <  1:3377677/100‑1 (MQ=255)                                                             tCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCtt                               <  1:1952944/100‑1 (MQ=255)                                                             cgatctcgtttATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCtt                               <  1:3225955/92‑1 (MQ=255)                                                             cgatctcgtttATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCta                               <  1:929293/92‑2 (MQ=255)                                                              cACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCttt                              <  1:3688227/100‑1 (MQ=255)                                                              cACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCttt                              >  1:1940999/1‑100 (MQ=255)                                                              cACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCttt                              <  1:4808062/100‑1 (MQ=255)                                                              cACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCtta                              <  1:2195005/100‑2 (MQ=255)                                                              atcttgATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCttt                              <  1:1563143/95‑1 (MQ=255)                                                              atcTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCttt                              <  1:4766136/98‑1 (MQ=255)                                                              atcTCGATCTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCttt                              <  1:3114016/98‑1 (MQ=255)                                                               aCTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCtggg                             <  1:1902239/100‑4 (MQ=255)                                                                cTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCtttta                            <  1:3941418/100‑3 (MQ=255)                                                                cTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAg                            <  1:4217128/100‑1 (MQ=255)                                                                 tcggcttATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAgg                           <  1:2034201/95‑1 (MQ=255)                                                                 tCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAgg                           <  1:2492511/100‑1 (MQ=255)                                                                   gatccataGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTACCAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGat                         <  1:4866086/95‑1 (MQ=255)                                                                   gATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGat                         <  1:2832683/100‑1 (MQ=255)                                                                   gATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTACAAAATCCGTACCTTTAGGat                         <  1:5210651/100‑1 (MQ=255)                                                                    aTTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGata                        <  1:412375/100‑1 (MQ=255)                                                                    aTTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGata                        <  1:776741/100‑1 (MQ=255)                                                                    aTTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGCTATATTTGCAAAATCCGTACCTTTAGGata                        <  1:2490912/100‑1 (MQ=255)                                                                           gTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTgg                 <  1:2174635/100‑2 (MQ=255)                                                                            tCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTc                <  1:659744/100‑1 (MQ=255)                                                                             cAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCt               <  1:2341287/100‑1 (MQ=255)                                                                              aaaTATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCtt              <  1:2822595/100‑1 (MQ=255)                                                                              aaaTATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCtt              <  1:3564434/100‑1 (MQ=255)                                                                              aaaTATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCtt              <  1:2785688/100‑1 (MQ=255)                                                                               aaTATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTa             <  1:2740054/100‑1 (MQ=255)                                                                                atatCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTag            <  1:505876/100‑2 (MQ=255)                                                                                      ttCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTcc      <  1:5489678/100‑1 (MQ=255)                                                                                      ttCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTcc      <  1:819446/100‑1 (MQ=255)                                                                                      ttCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTcc      <  1:3085609/100‑1 (MQ=255)                                                                                       tCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCa     <  1:4964766/100‑1 (MQ=255)                                                                                       tCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCa     <  1:3209333/100‑1 (MQ=255)                                                                                        cGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAGAGTCCag    <  1:331733/100‑2 (MQ=255)                                                                                          aGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCAttt  <  1:5112613/100‑1 (MQ=255)                                                                                          aGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCAttt  <  1:3655731/100‑1 (MQ=255)                                                                                                  |                                                                                            ACACAGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGCATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTT  >  NC_007793/1630964‑1631152

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑