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%	135.6 / NA	35	A48A (GCG→GCA)	intR	putative integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/15);  total (20/15)

ATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTGAAGTGG  >  NC_000913/1412852‑1413336                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                     ataACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTaaa                                                                                                                                                                                                                                             <  2:258896/250‑1 (MQ=255)              gATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCttttt                                                                                                                                                                                                                               >  2:1118489/1‑251 (MQ=255)                         aCTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGt                                                                                                                                                                                                                    <  1:1118489/251‑1 (MQ=255)                                                          ttGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGAc                                                                                                                                                                                   >  2:930023/1‑251 (MQ=255)                                                                             aTTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTACTGTTTCCCGAc                                                                                                                                                                                   >  2:1074568/1‑232 (MQ=255)                                                                             aTTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGAc                                                                                                                                                                                   <  1:1074568/232‑1 (MQ=255)                                                                             aTTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACAt                                                                                                                                                                <  1:1193209/251‑1 (MQ=255)                                                                                     tgttgtTAACTCTGTCTCTTTAATTTTTGTCCCGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAat                                                                                                                                                                                                                            >  2:397286/1‑183 (MQ=255)                                                                                     tgttgtTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAat                                                                                                                                                                                                                            <  1:397286/183‑1 (MQ=255)                                                                                                                      gATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAAt                                                                                                                                                                                                                                            <  1:865712/134‑1 (MQ=255)                                                                                                                      gATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAAt                                                                                                                                                                                                                                            >  2:865712/1‑134 (MQ=255)                                                                                                                      gATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTg                                                                                                                       >  2:627787/1‑251 (MQ=255)                                                                                                                       atatCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAAtc                                                                                                                                                                                                            >  1:728899/1‑165 (MQ=255)                                                                                                                       atatCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAAtc                                                                                                                                                                                                            <  2:728899/165‑1 (MQ=255)                                                                                                                         atCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTg                                                                                                                    >  1:118701/1‑251 (MQ=255)                                                                                                                                      ccGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACat                                                                                                       >  1:1153550/1‑251 (MQ=255)                                                                                                                                           cGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCAt                                                                                                  <  2:118701/251‑1 (MQ=255)                                                                                                                                              ttttATGACTCTCGTTGTCACCATTTTTGCCCAAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATg                                                                                                 >  1:815733/1‑249 (MQ=255)                                                                                                                                                       tctcGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGAt                                                                                       >  1:469067/1‑250 (MQ=255)                                                                                                                                                          cGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATaaa                                                                                    <  1:866088/250‑1 (MQ=255)                                                                                                                                                              gTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGAt                                                                               >  1:614456/1‑251 (MQ=255)                                                                                                                                                                    aTTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCt                                                                         <  2:815733/251‑1 (MQ=255)                                                                                                                                                                      ttttGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCttt                                                                       >  2:301691/1‑251 (MQ=255)                                                                                                                                                                                                   gTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATAATACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAAGCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTgg                                                                     <  1:930583/224‑1 (MQ=255)                                                                                                                                                                                                   gTCTTAAATAATCAAATTTACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCCGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTgg                                                                     >  2:930583/1‑224 (MQ=255)                                                                                                                                                                                                            aCTCAAATTCTCCGGAGTTTATTTCAGGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAACCTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTgg                                 <  2:474230/251‑1 (MQ=255)                                                                                                                                                                                                             cTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGc                                >  2:612635/1‑251 (MQ=255)                                                                                                                                                                                                              tCAAATTCACCGGAGTTTATTTCATGAACTATCACTGCTCTTAAATTTCCGGCCTTTTTACTATTACTGTTTGTAATCTCCCAGCCTTTTCATGTTTCCCGACCTCGTTTTCCTCGAAACCTGAACCAGCTGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCt                               >  1:1027648/1‑251 (MQ=255)                                                                                                                                                                                                                          gAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCt                                                                         >  1:1087882/1‑197 (MQ=255)                                                                                                                                                                                                                          gAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCt                                                                         <  2:1087882/197‑1 (MQ=255)                                                                                                                                                                                                                                  ttCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCtt                              <  1:346412/232‑1 (MQ=255)                                                                                                                                                                                                                                  ttCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCtt                              >  2:346412/1‑232 (MQ=255)                                                                                                                                                                                                                                     aTGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATc                                                  >  2:742201/1‑209 (MQ=255)                                                                                                                                                                                                                                     aTGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATc                                                  <  1:742201/209‑1 (MQ=255)                                                                                                                                                                                                                                            aTCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTCGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTGAAGTgg  >  2:1128959/1‑250 (MQ=255)                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                     ATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACTCGTTTGAAGTGG  >  NC_000913/1412852‑1413336

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑