Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	1,631,153	G→A	A48V (GCA→GTA)	SAUSA300_RS08060 ←	integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	1,631,153	0	G	A	100.0%	160.9 / NA	58	A48V (GCA→GTA)	SAUSA300_RS08060	integrase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (0/58);  total (0/58)

ATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTGCATTTTCAATAGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTCTTCAAATAGAGCAAACT  >  NC_007793/1631062‑1631249                                                                                            |                                                                                                 aTTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCa                                                                                          <  1:6481102/100‑1 (MQ=255) aTTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCa                                                                                          <  1:3422254/100‑1 (MQ=255)     aTTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAAtgg                                                                                      <  1:6131250/100‑3 (MQ=255)      tttGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGa                                                                                     <  1:2410425/100‑1 (MQ=255)        tGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAAtgggcg                                                                                   <  1:3608876/100‑6 (MQ=255)         gTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTCTCAATGGAAcc                                                                                  <  1:3039251/100‑1 (MQ=255)          tttAACAGCTTCATTTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGaaggt                                                                                 <  1:4833057/100‑4 (MQ=255)           ttAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCAc                                                                                <  1:2552031/100‑1 (MQ=255)             aaCAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGt                                                                              <  1:1662461/100‑1 (MQ=255)              aCAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGtt                                                                             <  1:3401966/100‑1 (MQ=255)              aCAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGta                                                                             <  1:1473253/100‑2 (MQ=255)               cAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTg                                                                            <  1:1098925/100‑1 (MQ=255)               cAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTg                                                                            <  1:5339829/100‑1 (MQ=255)               cAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTg                                                                            <  1:5360821/100‑1 (MQ=255)                aGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTgg                                                                           <  1:1241054/100‑2 (MQ=255)                 ttccgaTCTAATGGCTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                          <  1:6252848/95‑1 (MQ=255)                 gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                          <  1:2970687/100‑1 (MQ=255)                 gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                          <  1:4765343/100‑1 (MQ=255)                 gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                          <  1:4444697/100‑1 (MQ=255)                 gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                          <  1:5792740/100‑1 (MQ=255)                 gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                          <  1:3893965/100‑1 (MQ=255)                 gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                          <  1:5847675/100‑1 (MQ=255)                 gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                          <  1:6304031/100‑1 (MQ=255)                 gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGag                                                                          <  1:3321353/100‑2 (MQ=255)                     ctcttccgatcTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATgg                                                                      <  1:664440/90‑1 (MQ=255)                     cATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATgg                                                                      <  1:171917/100‑1 (MQ=255)                               cTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCatt                                                            <  1:3520884/100‑3 (MQ=255)                                ttttGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCaaag                                                           <  1:2298279/100‑2 (MQ=255)                                    gtgtTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACt                                                       <  1:2490203/100‑1 (MQ=255)                                      gtTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATATTCAATGGAACCACGTTGATATGGACAACCCAAATCACTaa                                                     <  1:6098955/100‑1 (MQ=255)                                             ttGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAaaataaat                                              <  1:597991/100‑1 (MQ=255)                                                cAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtact                                           <  1:6535345/100‑1 (MQ=255)                                                cAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtact                                           <  1:1186408/100‑1 (MQ=255)                                                 aaaaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCCCGTTGATCTGGCCAACCCAAATCACTAAAATAAAtacta                                          <  1:1416376/100‑1 (MQ=255)                                                  cgaTCTGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                         <  1:4820688/98‑1 (MQ=255)                                                  atctCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                         <  1:781456/97‑1 (MQ=255)                                                  aaaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                         <  1:4396636/100‑1 (MQ=255)                                                  aaaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                         <  1:2073659/100‑1 (MQ=255)                                                  aaaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                         <  1:3601007/100‑1 (MQ=255)                                                  aaaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                         <  1:4724697/100‑1 (MQ=255)                                                  aaaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                         <  1:4590160/100‑1 (MQ=255)                                                  aaaTCCGTACCTTTAGAATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                         <  1:4520443/100‑1 (MQ=255)                                                   aaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAca                                        <  1:6418795/100‑1 (MQ=255)                                                   aaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAca                                        <  1:4106258/100‑1 (MQ=255)                                                    tctcGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactactt                                       <  1:3280222/97‑3 (MQ=255)                                                    aTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAcat                                       <  1:5077870/100‑2 (MQ=255)                                                    aTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAcaa                                       <  1:3334960/100‑1 (MQ=255)                                                      ccGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAcaata                                     <  1:4531200/100‑2 (MQ=255)                                                          atcTTTGGGGTAATACTGGCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAcaattcaaa                                 <  1:6591561/98‑2 (MQ=255)                                                             tttAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAattcaattca                              <  1:383907/100‑1 (MQ=255)                                                                aGGTTAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAattcaattcagtg                           <  1:1218965/100‑4 (MQ=255)                                                                  gATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCAtctag                         <  1:1506892/100‑3 (MQ=255)                                                                           gTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATttgttc                <  1:5494852/100‑1 (MQ=255)                                                                           gTCTTAAAAGTCCACTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATttgttc                <  1:4894551/100‑1 (MQ=255)                                                                             cTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCat              <  1:5616264/100‑2 (MQ=255)                                                                                     tCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGcg      <  1:2258824/100‑2 (MQ=255)                                                                                         tttACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGcgtcgg  <  1:5253800/100‑6 (MQ=255)                                                                                         tttACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAAca  <  1:85563/100‑2 (MQ=255)                                                                                            |                                                                                                 ATTAATTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTGCATTTTCAATAGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTCTTCAAATAGAGCAAACT  >  NC_007793/1631062‑1631249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑