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	98.7%	196.0 / ‑4.9	75	A40A (GCA→GCG)	SAUSA300_RS08065	integrase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (2/72);  total (2/73)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

TCATCTGAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACTGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACGTGTTT  >  NC_007793/1631745‑1631925                                                                                                   |                                                                                   tCATCTGAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGc                                                                                  <  1:4610856/100‑1 (MQ=255) tCATCTGAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGc                                                                                  <  1:3221178/100‑1 (MQ=255)  cATCTGAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACTGc                                                                                  <  1:2213324/100‑1 (MQ=255)  cATCTGAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGca                                                                                 <  1:4366989/100‑1 (MQ=255)   aTCTGAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcac                                                                                <  1:2714126/100‑2 (MQ=255)    tCTGAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcatc                                                                               <  1:5543787/100‑1 (MQ=255)    tCTGAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcatc                                                                               <  1:5651660/100‑1 (MQ=255)    tCTGAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcata                                                                               <  1:2533747/100‑2 (MQ=255)      tGAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACTCCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcatcat                                                                             <  1:1611655/100‑1 (MQ=255)      tGAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcatcat                                                                             <  1:5735459/100‑1 (MQ=255)       gAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGcatcaga                                                                            >  1:4077919/1‑98 (MQ=255)       gAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCatcatc                                                                            <  1:3305395/100‑1 (MQ=255)       gAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCatcatc                                                                            <  1:3665432/100‑1 (MQ=255)       gAAATACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCatcatc                                                                            <  1:4081668/100‑1 (MQ=255)        aaaTACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCAtcatca                                                                           <  1:1202064/100‑1 (MQ=255)          aTACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAATACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACg                                                                         <  1:2397381/100‑1 (MQ=255)          aTACTACG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACg                                                                         <  1:1755993/100‑1 (MQ=255)            actacG‑GATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACgga                                                                       <  1:4022668/100‑3 (MQ=255)             tctacggATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACgcc                                                                       >  1:3405011/7‑98 (MQ=255)              ctacggATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAGAGAACCGCATCATCACGAcc                                                                      <  1:2569760/95‑1 (MQ=255)               tacggATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAGCAGAGCGCGTATTTACTTCTCTATAAAGAACCGCATCATCTCGACCt                                                                     <  1:2487844/96‑1 (MQ=255)               tacggATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCt                                                                     <  1:4342204/96‑1 (MQ=255)                acgggttttATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTa                                                                    <  1:4807396/95‑1 (MQ=255)                acggATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTa                                                                    <  1:3215483/97‑1 (MQ=255)                acggATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTa                                                                    <  1:3756405/97‑1 (MQ=255)                acggATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTa                                                                    <  1:3643827/97‑1 (MQ=255)                acggATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTa                                                                    <  1:4091992/97‑1 (MQ=255)                acggATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTa                                                                    <  1:5765937/97‑1 (MQ=255)                 cggATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTag                                                                   <  1:5474748/98‑2 (MQ=255)                  ggATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTaat                                                                  <  1:599905/99‑2 (MQ=255)                       ttATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCtt                                                             <  1:2165950/100‑1 (MQ=255)                       ttATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCtt                                                             <  1:4679173/100‑1 (MQ=255)                       tcttccgaTCTTCCTCAGCTAATGAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCtt                                                             <  1:5752413/93‑1 (MQ=255)                       tcttccgaTCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCtt                                                             <  1:3581492/93‑1 (MQ=255)                       tcttccgaTCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCtt                                                             <  1:5790912/93‑1 (MQ=255)                        tataGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCttt                                                            <  1:4062327/100‑2 (MQ=255)                         ttccgaTCTTCCTCGGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAg                                                           <  1:4849873/95‑1 (MQ=255)                         ttccgaTCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAg                                                           <  1:1932106/95‑1 (MQ=255)                         ataGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAg                                                           <  1:2709521/100‑1 (MQ=255)                                ccgatctaGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTg                                                    <  1:926245/93‑1 (MQ=255)                                cTTCCTTAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTg                                                    <  1:3004138/100‑1 (MQ=255)                                 ttCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTgg                                                   <  1:4853652/100‑2 (MQ=255)                                   gatctgCTAATAAAGGATTATAAACACCATCAACTGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGaag                                                 <  1:2519047/95‑2 (MQ=255)                                    cttaGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTACTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATccctcat                                                <  1:4454917/97‑7 (MQ=255)                                        gCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGt                                            <  1:1586433/100‑1 (MQ=255)                                           aataaAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTGAAATCTTAGAAATCTGAATGATGTTTa                                         <  1:536175/100‑1 (MQ=255)                                               aaGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAAcc                                     <  1:1807479/100‑1 (MQ=255)                                                              cATCAACAGAACGCTTATTTACTTCCCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACta                      <  1:4069692/100‑2 (MQ=255)                                                               aTCAACAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACttt                     <  1:1925689/100‑1 (MQ=255)                                                                  aaCAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCg                  <  1:4190721/100‑1 (MQ=255)                                                                  aaCAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCg                  <  1:5116824/100‑1 (MQ=255)                                                                  aaCAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCg                  <  1:1376212/100‑1 (MQ=255)                                                                  aaCAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCg                  <  1:490099/100‑1 (MQ=255)                                                                  aaCAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCg                  <  1:866424/100‑1 (MQ=255)                                                                  aaCAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCAGCATTTAAATACTTTGCg                  <  1:368882/100‑1 (MQ=255)                                                                  aaCAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATATGAATGATGTTTAAACCATCATTTAAATACTTTGCg                  <  1:183205/100‑1 (MQ=255)                                                                    cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGag                <  1:1583972/100‑2 (MQ=255)                                                                    cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                <  1:114949/100‑1 (MQ=255)                                                                    cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                <  1:3876672/100‑1 (MQ=255)                                                                    cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                <  1:2623037/100‑1 (MQ=255)                                                                    cAGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAt                <  1:2116909/100‑1 (MQ=255)                                                                     aGAACGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGAtg               <  1:2843710/100‑2 (MQ=255)                                                                        acgcggaTTTACTTCTCGATAAAGAACCTCATCATCACGACCTAGAATCTTAGAAATCTGTATGATGTTTAAACCATCTTTTAAATACTTTGCGATAGCt            <  1:5203672/94‑1 (MQ=255)                                                                        aCGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATATTTTGCGATAGCt            <  1:5268026/100‑1 (MQ=255)                                                                        aCGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCt            <  1:4709429/100‑1 (MQ=255)                                                                        aCGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCt            <  1:4430743/100‑1 (MQ=255)                                                                        aCGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCt            <  1:5713876/100‑1 (MQ=255)                                                                        aCGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCt            <  1:1136772/100‑1 (MQ=255)                                                                        aCGCTTATTTACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCt            <  1:1991174/100‑1 (MQ=255)                                                                               tttACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACgta     <  1:4516280/100‑2 (MQ=255)                                                                                ttACTACTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACgtat    <  1:1246078/100‑3 (MQ=255)                                                                                 tACTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACgtgta   <  1:978381/100‑2 (MQ=255)                                                                                  aCTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACGTGttg  <  1:1602237/100‑2 (MQ=255)                                                                                  aCTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACGTGttc  <  1:2528124/100‑2 (MQ=255)                                                                                  aCTTCTCTATAAAGAACCGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACGTGtta  <  1:4527996/100‑2 (MQ=255)                                                                                                   |                                                                                   TCATCTGAAATACTACGCGATTTTATAGCATCTTCCTCAGCTAATAAAGGATTATAAACACCATCAACAGAACGCTTATTTACTTCTCTATAAAGAACTGCATCATCACGACCTAAAATCTTAGAAATCTGAATGATGTTTAAACCATCATTTAAATACTTTGCGATAGCTAGACGTGTTT  >  NC_007793/1631745‑1631925

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: ‑