Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,413,092	C→T	A48A (GCG→GCA)	intR ←	putative integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,092	0	C	T	100.0%	124.9 / NA	36	A48A (GCG→GCA)	intR	putative integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (22/14);  total (22/14)

CGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTT  >  NC_000913/1412848‑1413329                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                              cGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTATCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCtt                                                                                                                                                                                                                                         >  1:252022/1‑251 (MQ=255) cGCTATAACGAATATGTGATATCGGCGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCtt                                                                                                                                                                                                                                         >  2:563791/1‑251 (MQ=255)     ataACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAAt                                                                                                                                                                                                                                     <  2:26444/251‑1 (MQ=255)           aaTATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCgg                                                                                                                                                                                                                               >  1:329730/1‑251 (MQ=255)             tatGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGcc                                                                                                                                                                                                                             >  1:201027/1‑251 (MQ=255)                gtgATATCGGGGTTCTTTCACAAATTATTATTCTTAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCtt                                                                                                                                                                                                                           <  2:557053/250‑1 (MQ=255)                gtgATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCtt                                                                                                                                                                                                                           <  2:212961/250‑1 (MQ=255)                                ttCACAAATTATTAGTCTGAGTGTTTTTAATTGTGACTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGATCGTTTTTATGACTATCGTTGTCACCATTTTAGCCCCAGAGCAGGAATGGGGATACCGTCTTAAATACTCATATTCACCGGAGTTTATTTAATGAAATATCAGTGATCTTAACTTTCCGGACTTTTTTATTTTACTGtatt                                                                                                                                                                                                          >  2:304867/1‑248 (MQ=255)                                                   aGTGCTTTTAATTGTGATTTTTTTTTCTCCATTGCGTTTGGAACTAATTCTGTCTCTTTAATTTTTGTCCAGATTTCACAAAGCTCTCCGAACGTTTTTATGACTTTCGTTGCCATCATTTTTCACCCAGTGCTGTACTGCTGATTACGTCTTAATTACTCAAATGTACCGGAGTTTATGTCATGAACTATCTGTGCCCTTAATTTTCTGCCCTATTTAATATTACTGTTTGTAATCTCCCCGTCttttt                                                                                                                                                                                        >  2:371513/1‑249 (MQ=255)                                                    gtttttttAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAAt                                                                                                                                                                                      <  2:415166/248‑1 (MQ=255)                                                                          tttCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCt                                                                                                                                                                 <  2:149954/250‑1 (MQ=255)                                                                           ttcttcATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGGTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTc                                                                                                                                                                <  1:545618/250‑1 (MQ=255)                                                                             cttcATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGCTAACACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCggtacgcatcatatcgcg                                                                                                                                                             >  1:317862/1‑234 (MQ=255)                                                                                cATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAAc                                                                                                                                                           >  1:450986/1‑250 (MQ=255)                                                                                          gttgttAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGAt                                                                                                                                                <  1:43100/251‑1 (MQ=255)                                                                                                               aTTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGt                                                                                                                                                                                    <  1:394545/194‑1 (MQ=255)                                                                                                               aTTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGt                                                                                                                                                                                    >  2:394545/1‑194 (MQ=255)                                                                                                                     gTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACNAGATGCGAATGTATCTACCTCTAATCTCGac                                                                                                                     >  2:289793/1‑251 (MQ=255)                                                                                                                              tCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTgg                                                                                                            >  1:378323/1‑251 (MQ=255)                                                                                                                                  aaaGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAATTACTCAAATTCCCCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTATTCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTNTCTACCTCTAATCTCGACACCTGTTGGTAAt                                                                                                        >  2:292326/1‑251 (MQ=255)                                                                                                                                           cGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACat                                                                                                >  1:560288/1‑250 (MQ=255)                                                                                                                                                               gTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACt                                                                           >  2:427665/1‑251 (MQ=255)                                                                                                                                                                  gTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGAt                                                                        >  1:111342/1‑251 (MQ=255)                                                                                                                                                                          ttttGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCtt                                                                 <  1:314173/250‑1 (MQ=255)                                                                                                                                                                            ttgacccAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAAGCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCGAATCTCGACACCTGTTGGTAATTTAGACATATCAGGAGTCTTTGATAAACTGATTTATCTTTg                                                               <  1:297987/246‑1 (MQ=255)                                                                                                                                                                               ccccAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGAt                                                            >  1:75840/1‑250 (MQ=255)                                                                                                                                                                                   aGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTATCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGCTTTATCTTTGGATAGttt                                                       >  2:397623/1‑250 (MQ=255)                                                                                                                                                                                         ggACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTAcc                                                   <  1:143601/249‑1 (MQ=255)                                                                                                                                                                                                 gAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATccc                                         <  1:348214/251‑1 (MQ=255)                                                                                                                                                                                                  aaaaCGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCt                                        >  2:563813/1‑251 (MQ=255)                                                                                                                                                                                                           tAAATACTAAAATTCACCGGAGTTTATTTCATGAACTATCAGTGATATTAAATTTCCGGCATTATTAATATTACTGTTTGTAATCTACCAGCCTTTTAATGTTTCCCGACATCGTTTTACTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCTACACCTGTTGGCAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGAACCAGATAATCCCTCGTTTGCTg                               >  2:128123/1‑251 (MQ=255)                                                                                                                                                                                                                   cAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCt                        <  1:305133/250‑1 (MQ=255)                                                                                                                                                                                                                     aaTTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTAc                     >  2:303970/1‑251 (MQ=255)                                                                                                                                                                                                                              gAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAgg              >  1:401406/1‑249 (MQ=255)                                                                                                                                                                                                                                       tCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGtt   >  1:353749/1‑251 (MQ=255)                                                                                                                                                                                                                                        cATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGttt  <  1:87734/251‑1 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                              CGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTT  >  NC_000913/1412848‑1413329

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑