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	100.0%	90.6 / NA	26	L113L (CTC→CTT)	intR	putative integrase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (15/11);  total (15/11)

TTTTTACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTG  >  NC_000913/1412665‑1413129                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                         tttttAATCCTTCAAATGGTTTGGTTGATATAAATCCAGACTGATACGCAAAAAGAAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGCGTTTTTAATTGTGAt                                                                                                                                                                                                                        >  1:202003/1‑251 (MQ=255)   tttACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGAtt                                                                                                                                                                                                                       <  1:103849/250‑1 (MQ=255)        tCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGttt                                                                                                                                                                                                                 >  2:130267/1‑251 (MQ=255)                                aaaTCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAAct                                                                                                                                                                                         <  2:290111/251‑1 (MQ=255)                                    cccGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGt                                                                                                                                                                                     >  2:300716/1‑251 (MQ=255)                                              aCGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAAtt                                                                                                                                                                           <  2:73645/251‑1 (MQ=255)                                                  aacaagCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTg                                                                                                                                                                       >  2:189191/6‑251 (MQ=255)                                                       gCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAg                                                                                                                                                                  <  1:118002/251‑1 (MQ=255)                                                                              atatAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGt                                                                                                                                           >  1:336046/1‑251 (MQ=255)                                                                                        cAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGAc                                                                                                                                  <  1:73969/250‑1 (MQ=255)                                                                                                       ttcttcCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCAtt                                                                                                                  >  2:149544/1‑251 (MQ=255)                                                                                                                   tgttgGATCTTGGATTATACAGGTAAAGCGTTTCTCAATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTg                                                                                                      >  2:241205/1‑251 (MQ=255)                                                                                                                        gATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTgg                                                                                                  >  1:279832/1‑250 (MQ=255)                                                                                                                           cTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTg                                                                                              >  2:7429/1‑251 (MQ=255)                                                                                                                                        ggTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGt                                                                                                       <  2:211794/229‑1 (MQ=255)                                                                                                                                        ggTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGt                                                                                                       >  1:211794/1‑229 (MQ=255)                                                                                                                                              gCGTTTCTCCATTCAGCAGTGCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTGCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTGTGGCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGCGAGAACGTCTTAAATAc                                                                           <  1:101891/251‑1 (MQ=255)                                                                                                                                                      ccATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTACCTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAGACGTCTTAAATACTCAAAt                                                                     <  2:202003/249‑1 (MQ=255)                                                                                                                                                          gcagcaGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCAcc                                                                <  1:172046/250‑1 (MQ=255)                                                                                                                                                                       ccGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCAt                                                  <  2:101657/251‑1 (MQ=255)                                                                                                                                                                                   gATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCATTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAgcg                                      >  2:175024/1‑251 (MQ=255)                                                                                                                                                                                        cGCTATAACGAATATGGGATATCGGGGTGCTTTCACATATTATTATTCTAAGTGTTTGGAATTGTGATTTCGGTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAAGTGTTGTCCAGATATCACAAAGTTCTCCGAACGTTTTTATGACTCTCGTTGTCGCCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCAGGAACGATTAGCGctct                                  <  2:348226/250‑1 (MQ=255)                                                                                                                                                                                         gCTATCACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCtt                                 >  2:180677/1‑250 (MQ=255)                                                                                                                                                                                           tataACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTaa                               >  1:264446/1‑250 (MQ=255)                                                                                                                                                                                           tataACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTATAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGATCTTaa                               >  2:320983/1‑250 (MQ=255)                                                                                                                                                                                                                       ttCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTg  >  2:276626/1‑251 (MQ=255)                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                         TTTTTACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTG  >  NC_000913/1412665‑1413129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑