Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	1,631,164	A→G	S44S (TCT→TCC)	SAUSA300_RS08060 ←	integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	1,631,164	0	A	G	100.0%	196.0 / NA	74	S44S (TCT→TCC)	SAUSA300_RS08060	integrase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (0/74);  total (0/74)

TTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTGCATTTTCAATAGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTCTTCAAATAGAGCAAACTCCTTACCTCTA  >  NC_007793/1631067‑1631260                                                                                                  |                                                                                                 tttGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGa                                                                                                <  1:2410425/100‑1 (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                                                                                       <  1:5339829/100‑1 (MQ=255)          cAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTg                                                                                       <  1:1098925/100‑1 (MQ=255)          cAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTg                                                                                       <  1:5360821/100‑1 (MQ=255)           aGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTgg                                                                                      <  1:1241054/100‑2 (MQ=255)            ttccgaTCTAATGGCTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                                     <  1:6252848/95‑1 (MQ=255)            gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                                     <  1:3893965/100‑1 (MQ=255)            gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                                     <  1:4444697/100‑1 (MQ=255)            gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                                     <  1:2970687/100‑1 (MQ=255)            gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                                     <  1:6304031/100‑1 (MQ=255)            gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                                     <  1:4765343/100‑1 (MQ=255)            gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                                     <  1:5847675/100‑1 (MQ=255)            gCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGat                                                                                     <  1:5792740/100‑1 (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                                                    <  1:3601007/100‑1 (MQ=255)                                             aaaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                                    <  1:4396636/100‑1 (MQ=255)                                             aaaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                                    <  1:2073659/100‑1 (MQ=255)                                             aaaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                                    <  1:4590160/100‑1 (MQ=255)                                             aaaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                                    <  1:4724697/100‑1 (MQ=255)                                             aaaTCCGTACCTTTAGAATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAAtactac                                                    <  1:4520443/100‑1 (MQ=255)                                              aaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAca                                                   <  1:4106258/100‑1 (MQ=255)                                              aaTCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTACATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTAca                                                   <  1:6418795/100‑1 (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)                                                                                        cATTTTCAATGGAATCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCtt         <  1:4798546/100‑1 (MQ=255)                                                                                        cATTTTCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCtt         <  1:6146213/100‑1 (MQ=255)                                                                                         aTTTTCAATGGAACTACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTa        <  1:4937813/100‑1 (MQ=255)                                                                                          ttttCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTAc       <  1:3575429/100‑1 (MQ=255)                                                                                           tttCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTAcc      <  1:3317466/100‑1 (MQ=255)                                                                                            ttCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTAccc     <  1:623127/100‑2 (MQ=255)                                                                                            ttCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTACct     <  1:843346/100‑1 (MQ=255)                                                                                            ttCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTACct     <  1:5300910/100‑1 (MQ=255)                                                                                             tCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTAccag    <  1:3918626/100‑3 (MQ=255)                                                                                             tCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTACctg    <  1:999421/100‑2 (MQ=255)                                                                                             tCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTACctc    <  1:1656270/100‑1 (MQ=255)                                                                                             tCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTACctc    <  1:5725119/100‑1 (MQ=255)                                                                                             tCAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTACcta    <  1:4588255/100‑2 (MQ=255)                                                                                              cAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTAccatg   <  1:5361800/100‑4 (MQ=255)                                                                                              cAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTACctct   <  1:3658229/100‑1 (MQ=255)                                                                                              cAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTACctct   <  1:3880056/100‑1 (MQ=255)                                                                                              cAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTACctct   <  1:1272068/100‑1 (MQ=255)                                                                                              cAATGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTACctct   <  1:773519/100‑1 (MQ=255)                                                                                               aaTGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTAcccaag  <  1:5306849/100‑5 (MQ=255)                                                                                               aaTGGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTGTTCAAATAGAGCGAACTCCTTAccagct  <  1:4436747/100‑5 (MQ=255)                                                                                                  |                                                                                                 TTTGTTTAACAGCTTCATCTAATGACTTTTGTGTTATATTTGCAAAATCCGTACCTTTAGGATAATACTGTCTTAAAAGTCCATTTGCATTTTCAATAGAACCACGTTGATATGGACAACCCAAATCACTAAAATAAATACTACAATTCAATTCATCTTCTATTTCTTCAAATAGAGCAAACTCCTTACCTCTA  >  NC_007793/1631067‑1631260

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: ‑