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%	183.4 / NA	67	A79T (GCA→ACA)	SAUSA300_RS08060	integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (1/66);  total (1/66)

ACACAGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGCATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTT  >  NC_007793/1630964‑1631152                                                                                                  |                                                                                            acacaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAt                                                                                           <  1:3952876/100‑1 (MQ=255) acacaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAt                                                                                           <  1:5711634/100‑1 (MQ=255)  cacaGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTAta                                                                                          <  1:3501460/100‑2 (MQ=255)          tttAATATAGGTTCCCAATTTTGTGTGCTTCCATGGTACTTTAGCATTTCCTCCCTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGtt                                                                                  <  1:4649806/100‑1 (MQ=255)          tttAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGtt                                                                                  <  1:5427730/100‑1 (MQ=255)          tttAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGtt                                                                                  <  1:1648551/100‑1 (MQ=255)           ttAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGttt                                                                                 <  1:5739796/100‑1 (MQ=255)           ttAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGttt                                                                                 <  1:5653793/100‑1 (MQ=255)           ttAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGttt                                                                                 <  1:174570/100‑1 (MQ=255)            tAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTa                                                                                <  1:6115292/100‑1 (MQ=255)              atatAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAAc                                                                              <  1:6028779/100‑1 (MQ=255)              atatAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAAc                                                                              <  1:2043514/100‑1 (MQ=255)              atatAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAAc                                                                              <  1:6630935/100‑1 (MQ=255)                ataGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAg                                                                            <  1:1339323/100‑1 (MQ=255)                 taGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGc                                                                           <  1:1147572/100‑1 (MQ=255)                  aGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCt                                                                          <  1:1398735/100‑1 (MQ=255)                   ggTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCGCTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTCTAACAGCta                                                                         <  1:2851726/100‑2 (MQ=255)                   ggTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCtt                                                                         <  1:5467696/100‑1 (MQ=255)                   ggTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCtt                                                                         <  1:410566/100‑1 (MQ=255)                   ggTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCtt                                                                         <  1:6542546/100‑1 (MQ=255)                     ttCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTGGTTTAACAgggtcc                                                                       <  1:5387336/100‑6 (MQ=255)                         caATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTGAACAGCTTCATCTa                                                                   <  1:4594285/100‑1 (MQ=255)                                gtgtgCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGCGTATTAATTTGTTTAACAGCTTCATCTAATGAccc                                                            <  1:3776372/100‑3 (MQ=255)                                       tACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTgtgta                                                     <  1:2554091/100‑2 (MQ=255)                                       tACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGtt                                                     <  1:2799583/100‑1 (MQ=255)                                       tACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTAGTTTAACAGCGTCATCTAATGACTTTTGTGtt                                                     <  1:4863868/100‑1 (MQ=255)                                               aCTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGc                                             <  1:928464/100‑1 (MQ=255)                                                 tttAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTGACAGCTTCATCTAATGACTTTTGTGTTATATGTGCaa                                           <  1:2463801/100‑1 (MQ=255)                                                  ttAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCaag                                          <  1:5964743/100‑2 (MQ=255)                                                            cTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCt                                <  1:2588174/100‑1 (MQ=255)                                                             tCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTAccag                               <  1:2136755/100‑3 (MQ=255)                                                              cACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCttt                              <  1:4368128/100‑1 (MQ=255)                                                              cACTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCttt                              <  1:1664621/100‑1 (MQ=255)                                                              cACTCGATTTATAGGCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCttt                              <  1:4985872/100‑1 (MQ=255)                                                               tctcattttATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCtttt                             <  1:5598879/94‑2 (MQ=255)                                                                cTCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTat                            <  1:5625070/100‑2 (MQ=255)                                                                 tCGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAgg                           <  1:745080/100‑1 (MQ=255)                                                                  tagtctataGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGa                          >  1:409194/6‑100 (MQ=255)                                                                  cGATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGa                          <  1:6239735/100‑1 (MQ=255)                                                                   gATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGGCTTTTGTGTTATATTTGCAAAATCCGTGCCTTTAGGat                         <  1:6092203/100‑1 (MQ=255)                                                                   gATTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGat                         <  1:5254068/100‑1 (MQ=255)                                                                   gATTTATAGTCAAAGATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGat                         <  1:4855420/100‑1 (MQ=255)                                                                   gATTCATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGat                         <  1:1594011/100‑1 (MQ=255)                                                                    aTTTATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGata                        <  1:4064325/100‑1 (MQ=255)                                                                     tttATAGTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGatag                       <  1:5434692/100‑2 (MQ=255)                                                                           gTCAAATATCATTCGATGCCGTGTATTAATTTGTTTAACAGCTTCATTTAATGACTTTTGTTTTATATTTGCAAAATCCGTACCTTTAGGATAATACTgc                 <  1:5873896/100‑2 (MQ=255)                                                                           gTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTgg                 <  1:1889161/100‑2 (MQ=255)                                                                           gTCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTATTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTgg                 <  1:1368516/100‑2 (MQ=255)                                                                            tCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTggg                <  1:445014/100‑3 (MQ=255)                                                                            tCAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTc                <  1:5173154/100‑1 (MQ=255)                                                                             cAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTca               <  1:1661805/100‑2 (MQ=255)                                                                             cAAATATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTAGATTTGCAAAATCCGTACCTTTAGGATAATACTGTca               <  1:5056403/100‑2 (MQ=255)                                                                              aaaTATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCtt              <  1:6497191/100‑1 (MQ=255)                                                                              aaaTATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCtt              <  1:238961/100‑1 (MQ=255)                                                                              aaaTATCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCtt              <  1:3686801/100‑1 (MQ=255)                                                                                atatCATTCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTag            <  1:3107157/100‑2 (MQ=255)                                                                                      ttCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTcc      <  1:593491/100‑1 (MQ=255)                                                                                      ttCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTcc      <  1:1927323/100‑1 (MQ=255)                                                                                       tCGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCa     <  1:6474765/100‑1 (MQ=255)                                                                                        cGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCAt    <  1:3452269/100‑1 (MQ=255)                                                                                        cGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCAt    <  1:6434478/100‑1 (MQ=255)                                                                                        cGAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCAt    <  1:6529993/100‑1 (MQ=255)                                                                                         gAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCAtt   <  1:6650854/100‑1 (MQ=255)                                                                                         gAGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTAGATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCAtt   <  1:4820571/100‑1 (MQ=255)                                                                                          aGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCAttt  <  1:1297840/100‑1 (MQ=255)                                                                                          aGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCAttt  <  1:1322298/100‑1 (MQ=255)                                                                                          aGGCCGTGTATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCAttt  <  1:2032066/100‑1 (MQ=255)                                                                                                  |                                                                                            ACACAGTCATTTAATATAGGTTCACAATTTTGTGTGCTTACATGGTACTTTAGCATTTCCTCACTCGATTTATAGTCAAATATCATTCGAGGCCGTGCATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTT  >  NC_007793/1630964‑1631152

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: ‑