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%	131.5 / NA	33	A48A (GCG→GCA)	intR	putative integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (16/17);  total (16/17)

ATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACT  >  NC_000913/1412846‑1413324                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                         atCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGct                                                                                                                                                                                                                                       <  1:240988/250‑1 (MQ=255)    gCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCtt                                                                                                                                                                                                                                    >  2:340191/1‑250 (MQ=255)                  gtgATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCttt                                                                                                                                                                                                                     >  2:92246/1‑251 (MQ=255)                       atCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAat                                                                                                                                                                                                                >  1:12216/1‑251 (MQ=255)                                      caAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAAt                                                                                                                                                                                                 <  1:273107/251‑1 (MQ=255)                                                 tCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCACAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCtt                                                                                                                                                                                      >  2:343495/1‑251 (MQ=255)                                                          ttttAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGtt                                                                                                                                                                              <  2:179325/250‑1 (MQ=255)                                                              aaTTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCCCCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTccc                                                                                                                                                                          <  2:222266/250‑1 (MQ=255)                                                              aaTTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCTAGCCTTTTACTGTTTCCCg                                                                                                                                                                         >  2:120234/1‑251 (MQ=255)                                                                       ttCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGTGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGttt                                                                                                                                                                >  2:188444/1‑251 (MQ=255)                                                                                  cATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAAc                                                                                                                                                      <  2:260635/250‑1 (MQ=255)                                                                                      gtgtTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGa                                                                                                                                                  >  2:290981/1‑250 (MQ=255)                                                                                          ttgttgTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAAcc                                                                                                                                               >  1:76675/1‑249 (MQ=255)                                                                                           tgttgtTAAGTCTGTCTCTTTAATTTTTGTCCAAATATCACAAAGCTCTCCGAAAGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAAcc                                                                                                                                               >  1:288261/1‑248 (MQ=255)                                                                                              tgttAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATg                                                                                                                                          <  2:53501/250‑1 (MQ=255)                                                                                                 tAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGa                                                                                                                                       >  2:42523/1‑250 (MQ=255)                                                                                                        gTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCt                                                                                                                               >  2:42964/1‑251 (MQ=255)                                                                                                                aaTTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTa                                                                                                                        <  2:368175/250‑1 (MQ=255)                                                                                                                  tttttGTGCAGATATCACCAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGTAAACGTCTTAAATACTCAAATTCAACGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGACCCAGATGCGAATGTATCTACCTCTAAtc                                                                                                                     >  2:151457/1‑251 (MQ=255)                                                                                                                     ttGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAAtctc                                                                                                                   <  2:335300/250‑1 (MQ=255)                                                                                                                      tGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACAGCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCg                                                                                                                  <  1:128060/250‑1 (MQ=255)                                                                                                                       gTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCAAGTGCTGGACTGGGGCAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGac                                                                                                                >  1:124435/1‑251 (MQ=255)                                                                                                                                   caAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTaa                                                                                                    <  2:340981/251‑1 (MQ=255)                                                                                                                                          ctcCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAg                                                                                               <  2:179988/249‑1 (MQ=255)                                                                                                                                                        aTGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCt                                                                                <  1:44295/250‑1 (MQ=255)                                                                                                                                                          gACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTg                                                                             <  1:329187/251‑1 (MQ=255)                                                                                                                                                                 gTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACt                                                                      <  1:343495/251‑1 (MQ=255)                                                                                                                                                                                            gACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGa                                           <  1:160298/251‑1 (MQ=255)                                                                                                                                                                                                   gAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATccc                                    >  1:233710/1‑251 (MQ=255)                                                                                                                                                                                                            ttAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCt                           >  1:68500/1‑251 (MQ=255)                                                                                                                                                                                                             tAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTg                             <  1:22596/248‑1 (MQ=255)                                                                                                                                                                                                                     cAAATTCACCGGAGTTTATTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCtt                  >  1:11100/1‑251 (MQ=255)                                                                                                                                                                                                                                      aTTTCATGAACTATCAGTGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACt  <  2:242176/250‑1 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                         ATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACACCTGTTGGTAATTTAGACATATCATGAGTCTTTGATAAACTGATTTATCTTTGGATAGTTGTACCAGATAATCCCTCGTTTGCTGTCTGGCTTACCTAAAGGAGATACT  >  NC_000913/1412846‑1413324

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑