Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	2,127,043	T→C	N144N (AAT→AAC)	SAUSA300_RS10835 →	integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	2,127,043	0	T	C	100.0%	143.3 / NA	56	N144N (AAT→AAC)	SAUSA300_RS10835	integrase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (41/15);  total (41/15)

CAAAAGAACACGCAAAAGAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGGCTTATTTTTAAAAATCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAATATGAAATACTAAA  >  NC_007793/2126949‑2127132                                                                                               |                                                                                          cAAAAGAACACGCAAAAGAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGc                                                                                      >  1:834577/1‑100 (MQ=255)     aGAACACGCAAAAGAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAAccccagatcg                                                                                  >  1:3932306/1‑94 (MQ=255)     aGAACACGCAAAAGAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTtat                                                                                  >  1:3763222/1‑100 (MQ=255)       tacacGCAAAAGAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATaa                                                                                >  1:3702579/2‑100 (MQ=255)       cacacGCAAAAGAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATaa                                                                                >  1:4080657/2‑100 (MQ=255)       agcacacaAAAGAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATaa                                                                                >  1:554845/3‑100 (MQ=255)       aaCACGCAAAAGAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATaa                                                                                >  1:4582461/1‑100 (MQ=255)       aaCACGCAAAAGAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATaa                                                                                >  1:5665601/1‑100 (MQ=255)         cacGCAAAAGAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAg                                                                              >  1:2265846/1‑100 (MQ=255)                ctgAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATta                                                                       >  1:4879465/3‑100 (MQ=255)                    caCTATAAGAAAAAAAAACGGTGCTATTCGGTCAACTTTAGATGACGCATTATATGATAGACTTATTTTTAAAAACAGCGCTTATAAAGTTAATTATaat                                                                   >  1:3709852/2‑99 (MQ=255)                               aaacaaacGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAAcc                                                        >  1:337925/1‑100 (MQ=255)                                aacaaacGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGATAATTATAAAGCCGGAAAACCt                                                       >  1:4145457/1‑100 (MQ=255)                                  accccGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTAc                                                     >  1:2724519/5‑100 (MQ=255)                                  aaaacGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTAc                                                     >  1:2285237/2‑100 (MQ=255)                                   aaacGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACg                                                    >  1:4182042/1‑100 (MQ=255)                                       ggTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGt                                                >  1:59201/1‑100 (MQ=255)                                         tGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCa                                              >  1:4100824/1‑100 (MQ=255)                                          gCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAg                                             >  1:4673771/1‑100 (MQ=255)                                          gCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAg                                             >  1:1319957/1‑100 (MQ=255)                                           cTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGa                                            >  1:2683125/1‑100 (MQ=255)                                           cTATTCGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGa                                            >  1:957165/1‑100 (MQ=255)                                              tccgatctgCTTTGGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACa                                         <  1:3180731/92‑1 (MQ=255)                                                tggTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAg                                       <  1:4934566/99‑1 (MQ=255)                                                cGGTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTCAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAg                                       >  1:5412120/1‑100 (MQ=255)                                                 ggTCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGa                                      >  1:2071485/1‑100 (MQ=255)                                                  ctCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGaa                                     >  1:3704683/2‑100 (MQ=255)                                                   tCAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGaaa                                    >  1:1669399/1‑100 (MQ=255)                                                    cAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAATCTACGAAGTCATAACAAGaaaa                                   >  1:901865/1‑100 (MQ=255)                                                    cAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGaaaa                                   >  1:266259/1‑100 (MQ=255)                                                    cAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGaaaa                                   >  1:417969/1‑100 (MQ=255)                                                    cAGCTTTAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGaaaa                                   >  1:1191880/1‑100 (MQ=255)                                                         ttAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCa                              >  1:5057695/1‑100 (MQ=255)                                                          tAGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCAt                             >  1:969621/1‑100 (MQ=255)                                                           aGATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCAtc                            >  1:163419/1‑100 (MQ=255)                                                            gATGACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCAtct                           <  1:5491389/100‑1 (MQ=255)                                                             ccgACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCAtctc                          >  1:4565599/3‑100 (MQ=255)                                                              cgACGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCg                         >  1:5129797/2‑100 (MQ=255)                                                                aCGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGt                       <  1:4865232/100‑1 (MQ=255)                                                                 cGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCggaa                      >  1:4563824/1‑98 (MQ=255)                                                                 cGCATTATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTa                      <  1:1698544/100‑1 (MQ=255)                                                                     ttATATGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTg                  <  1:1243939/100‑1 (MQ=255)                                                                      tctatGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGa                 >  1:2757786/3‑100 (MQ=255)                                                                      tataTGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGa                 >  1:3297957/1‑100 (MQ=255)                                                                      tataTGATGGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGa                 <  1:2138915/100‑1 (MQ=255)                                                                      tataTGATGGACTTATTTTTAAAAACCCCGCATATAAAGTTAATTATAAAGCCGGAAAACCTATGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGa                 <  1:609298/100‑1 (MQ=255)                                                                         atgatgGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAata              >  1:2196667/1‑100 (MQ=255)                                                                           gatgGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAATATg            >  1:3812398/1‑100 (MQ=255)                                                                           gatgGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAATATg            >  1:854625/1‑100 (MQ=255)                                                                           gatgGACTTATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAATATg            >  1:4134857/1‑100 (MQ=255)                                                                                   tATTTTTAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAATATGAAATACTa    <  1:4397556/100‑1 (MQ=255)                                                                                     tttttAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAATATGAAATACTaaa  <  1:3186976/100‑1 (MQ=255)                                                                                     tttttAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAATATGAAATACTaaa  <  1:5451860/100‑1 (MQ=255)                                                                                     tttttAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAATATGAAATACTaaa  <  1:55576/100‑1 (MQ=255)                                                                                     tttttAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAATATGAAATACTaaa  <  1:1878831/100‑1 (MQ=255)                                                                                     tttttAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAATATGAAATACTaaa  <  1:4263943/100‑1 (MQ=255)                                                                                     tttttAAAAACCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACGGAATATGAAATACTaaa  <  1:2549055/100‑1 (MQ=255)                                                                                               |                                                                                          CAAAAGAACACGCAAAAGAAACTATAAGAAAAACAAACGGTGCTATTCGGTCAGCTTTAGATGACGCATTATATGATGGGCTTATTTTTAAAAATCCCGCTTATAAAGTTAATTATAAAGCCGGAAAACCTACGAAGTCAGAACAAGAAAAATTCATCTCGGTAACTGAATATGAAATACTAAA  >  NC_007793/2126949‑2127132

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑