Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,412,897	G→A	L113L (CTC→CTT)	intR ←	putative integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,412,897	0	G	A	97.1%	98.4 / NA	34	L113L (CTC→CTT)	intR	putative integrase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (15/18);  minor base C (1/0);  total (16/18)
Fisher's exact test for biased strand distribution p-value = 4.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.72e-01

TCGCTGTAATTTTTTTACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCC  >  NC_000913/1412654‑1413138                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                  tCGCTGTAATTTTTTTACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGtt                                                                                                                                                                                                                                             <  1:40785/250‑1 (MQ=255)              tttACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGAtt                                                                                                                                                                                                                                <  2:381480/250‑1 (MQ=255)                           aTGGTTTGGTTGATATAAATCCCGCCTGATACGCACAACGCAACAGCGAACCGAGCAGGGCGATCTAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCCGCAGTTCATTCCGGTAGTTTAAGATATAGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGAGTTTTTAATTGTGATTTCGTTTTCTTCAtt                                                                                                                                                                                                                  >  2:164623/1‑251 (MQ=255)                                  ggttGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGtgtttg                                                                                                                                                                                                           >  1:292783/1‑251 (MQ=255)                                                       aTACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTATGCGCACGCTCATTCCTTTTTTGTTGGCACTTGGATTATCCAGGCAAAGCGTTTCTCCATGCAGAAGTTCATTCCGGTAGTTTAAGCTATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTa                                                                                                                                                                                       >  1:219242/1‑250 (MQ=255)                                                              aaaCGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGt                                                                                                                                                                               >  1:463321/1‑251 (MQ=255)                                                                 cGCAACAGCGAACAGAGCCGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTCATTCTTGGATCTTGGCTTATCCCGGTAAAGCGTTTATCCAAGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGAGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTcc                                                                                                                                                                             >  1:65643/1‑250 (MQ=255)                                                                       aGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCATTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTTTCTCTTTAAGTTTAGTCCAGATATc                                                                                                                                                                      <  1:111846/251‑1 (MQ=255)                                                                                     ggCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAAt                                                                                                                                                                                     >  1:8486/1‑222 (MQ=255)                                                                                     ggCGATATAGTTAGCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAAt                                                                                                                                                                                     <  2:8486/222‑1 (MQ=255)                                                                                        gATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACg                                                                                                                                                     <  1:64909/251‑1 (MQ=255)                                                                                                tATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGCATATGTGATATCGGGGTACTTTCACAAATTATTATTCTCAGAGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATg                                                                                                                                             >  2:147716/1‑251 (MQ=255)                                                                                                 aTCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTTTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATg                                                                                                                                             >  2:257540/1‑250 (MQ=255)                                                                                                          gcgcACGGTTGTTCCTTTCTTGGATGATCTTTGATTATCCATGTAAAGCGGTTCTCCATTCAGCAGTTCATACCGGTAGTTTAAGATATCGCGATAACGAATATGTTATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCAGTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCCCTCCGAACGCTTTTATGACTCTCGtt                                                                                                                                    <  2:125358/250‑1 (MQ=255)                                                                                                          gcgcACGGTTCTTCCTTTTTTGGTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGtt                                                                                                                                    <  1:2466/250‑1 (MQ=255)                                                                                                                        cTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGcc                                                                                                                     >  1:152969/1‑251 (MQ=255)                                                                                                                        cTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGcc                                                                                                                     >  1:171600/1‑251 (MQ=255)                                                                                                                              tgttgGGTCTTGGATTATCCAGGTAAAGCGGTTCTCCATGCAGCAGTTCATGCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCATAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTGGCCCCAGt                                                                                                                <  2:106927/250‑1 (MQ=255)                                                                                                                                         ggATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTggg                                                                                                     <  1:363102/250‑1 (MQ=255)                                                                                                                                               tCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGcc                                                                                                                     >  1:390824/1‑228 (MQ=255)                                                                                                                                               tCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGcc                                                                                                                     <  2:390824/228‑1 (MQ=255)                                                                                                                                                 cAGGTAAAGCGTTTCTCCATGCAGCATTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTTATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGct                                                                                                                                                              <  2:383093/185‑1 (MQ=255)                                                                                                                                                 cAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGct                                                                                                                                                              >  1:383093/1‑185 (MQ=255)                                                                                                                                                      aaaGCGTTTCCCCATGCAGCAGTTCATTCCTGTATTTTAAGATATCTCTATAACGAATATGTGATATCGTGGTACTTTCACAAATTATTATTCTAAGTGGTTTTAAGTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGCCTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTaaa                                                                                       <  2:247770/251‑1 (MQ=255)                                                                                                                                                                                       aGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTAACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACt                                                      >  2:277191/1‑251 (MQ=255)                                                                                                                                                                                          ttAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATc                                                   >  1:12078/1‑251 (MQ=255)                                                                                                                                                                                                    gCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTa                                         <  1:356882/251‑1 (MQ=255)                                                                                                                                                                                                          aCGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTc                                   >  2:4614/1‑251 (MQ=255)                                                                                                                                                                                                                     atatCGGGGTACTTTCCCAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAACTACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTCAATTTCCGGCCttttt                         >  1:316513/1‑250 (MQ=255)                                                                                                                                                                                                                                   tCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGGGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCGCTTAAATTTCCGGCCTTTTTAATATTACTGTTTg           <  2:171600/250‑1 (MQ=255)                                                                                                                                                                                                                                        aaTTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAAtct     <  1:375528/251‑1 (MQ=255)                                                                                                                                                                                                                                           tattattCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCACTGTGTTTGTTGTTAACTCTGTCTCTTGAATTTTGGTCCAGATATCACAAAGCTCTCCGACCTTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGTTAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCATCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTcc   <  2:21568/250‑1 (MQ=255)                                                                                                                                                                                                                                            attattCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTccc  <  1:315390/250‑1 (MQ=255)                                                                                                                                                                                                                                            attattCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATGTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTGTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTTCGGCCTTTTTAATATTACTGTTTGTAAtctctc  <  1:315376/250‑3 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                  TCGCTGTAATTTTTTTACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATCTCCC  >  NC_000913/1412654‑1413138

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑