Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,412,163	C→T	R358Q (CGG→CAG)	intR ←	putative integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,412,163	0	C	T	100.0%	126.1 / NA	36	R358Q (CGG→CAG)	intR	putative integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (16/20);  total (16/20)

TCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGCAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTAT  >  NC_000913/1411917‑1412375                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                     tctttcttTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGTGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACACCCAGCAGACAAAAGTATGCTGCGt                                                                                                                                                                                                                  >  2:383406/1‑251 (MQ=255)                            tGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATAcc                                                                                                                                                                                       >  1:246059/1‑251 (MQ=255)                                 tattTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCAc                                                                                                                                                                                  >  1:332341/1‑251 (MQ=255)                                    ttCAGTTCTCTGGTACTAAATGGGGCAAATTGAGGGCAAACTTTGCAACTACGATAACCGCGCATTCACCATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGtt                                                                                                                                                                               >  1:250762/1‑251 (MQ=255)                                                  aCTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATACCCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTc                                                                                                                                                                 <  1:289296/251‑1 (MQ=255)                                                  aCTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTc                                                                                                                                                                 <  2:181506/251‑1 (MQ=255)                                                                aTTGGGGGCAAACTTTGCAACTACGATAACCGAGCATTCAACATGGCTATCTGTTAGTCGTTCATGTCATCAATCCCCATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTCTAAATGCCGGGTTCGCTCCTGCCGTCACCAGCCAGCAGGCAAAAGTATGCTGCGTCTGGTACGGATTACGCCGGCGAATACCCGCACGTTTTTCTGCTGCATTCCACCTTGCCCCCa                                                                                                                                                    >  2:209003/1‑250 (MQ=255)                                                                       gCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCtt                                                                                                                                            <  2:155079/251‑1 (MQ=255)                                                                       gCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCtt                                                                                                                                            >  2:140161/1‑251 (MQ=255)                                                                                       cGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATCCACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGtt                                                                                                                            >  2:235098/1‑251 (MQ=255)                                                                                         aTAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCAAATACTGTAAATTTCATACACCATCTGTGCAGTTTCATGCCCCATTTGGCTGGCTATCAATGACGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCACAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATAACAGCACGTTTTACTGCTGCATTCACCCTTGCCCCCAAACTGCTTCACGAGTAATAAGGtttt                                                                                                                          >  1:179562/1‑251 (MQ=255)                                                                                                 gcATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGt                                                                                                                                                                                <  2:404073/189‑1 (MQ=255)                                                                                                 gcATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGt                                                                                                                                                                                >  1:404073/1‑189 (MQ=255)                                                                                                      cAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCCGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGTCGAATACCAGCACGTTTTACTTCTGCATTCCACCTTGCCCCCACACTGCTTACCGGGAAATAAGGTTTTTGTTTTCCGTTac                                                                                                             >  2:212687/1‑251 (MQ=255)                                                                                                             gCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCt                                                                                                      <  2:189233/251‑1 (MQ=255)                                                                                                                        gtcgtTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGaaaa                                                                                           <  1:140161/251‑1 (MQ=255)                                                                                                                         tcgtTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGtaa                                                                                                                                   <  2:394547/210‑1 (MQ=255)                                                                                                                         tcgtTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGtaa                                                                                                                                   >  1:394547/1‑210 (MQ=255)                                                                                                                          cgtTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACa                                                                                         <  2:137278/251‑1 (MQ=255)                                                                                                                               aTGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATg                                                                                    <  1:248745/251‑1 (MQ=255)                                                                                                                                   catcaATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTGCCGTTACACACCCTGGGCATGAAAACAAAATGTAGt                                                                                <  2:94332/251‑1 (MQ=255)                                                                                                                                    atcaATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGtt                                                                               <  1:249499/251‑1 (MQ=255)                                                                                                                                                      aaTTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGc                                                             <  2:332341/251‑1 (MQ=255)                                                                                                                                                          tCATACACCATCTGCGCATTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGt                                                          <  1:354203/250‑1 (MQ=255)                                                                                                                                                          tCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGt                                                          <  1:90913/250‑1 (MQ=255)                                                                                                                                                              acacCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTcc                                                     >  2:373637/1‑251 (MQ=255)                                                                                                                                                                       gcgcAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTGTTGGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGGTCTGCCGTACTCCCGATGATa                                             <  2:200797/250‑1 (MQ=255)                                                                                                                                                                            gTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGt                                       <  1:195592/251‑1 (MQ=255)                                                                                                                                                                                       cATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGttt                                                                                                                           <  1:407029/156‑1 (MQ=255)                                                                                                                                                                                       cATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCAGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGttt                                                                                                                           >  2:407029/1‑156 (MQ=255)                                                                                                                                                                                                 gctATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGatgatg                  >  1:325848/1‑251 (MQ=255)                                                                                                                                                                                                 gctATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGatgatg                  <  1:23184/251‑1 (MQ=255)                                                                                                                                                                                                             gggTTCTCGCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCTCCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGAGAAAAGGTGATTTCGCTTTTGCGATGATGCCCTGTCAGttt      <  2:253751/251‑1 (MQ=255)                                                                                                                                                                                                                 tCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTAt  >  1:155806/1‑251 (MQ=255)                                                                                                                                                                                                                                aCAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGAt                                    <  1:253016/202‑1 (MQ=255)                                                                                                                                                                                                                                aCAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGAt                                    >  2:253016/1‑202 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                     TCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGCAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTAT  >  NC_000913/1411917‑1412375

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑