Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,135,387	C→T	E104K (GAA→AAA)	unknown ←	Type IV secretion system protein VirD4

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,135,387	0	C	T	100.0%	86.0 / NA	33	E104K (GAA→AAA)	unknown	Type IV secretion system protein VirD4
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (16/17);  total (16/17)

CGATAGACTTTTTGCCCCAATATTTTTTGACGGTATTTACTGGTGATACGATAGCATTCGTTTTTAATGTCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACGAATTGCGCACCGATAAAGCGTAAAAGTTTTTTGCCGAGCTTGCCGACGATAATGCCGTTTTCTTCTTCCATCAAGCCCATTTCCCGCGCTTCCGAGGCAGTCGCAAATTCGGCGTTACCATAAAGATTCTTTTTAGGCTGATAGAAGAGTTTCAGCATAATCAGTAGGCAGACGACAAAACTAATCAATAAG‑GATTGCCAGATTTTCGGATAA  >  1/1135164‑1135538                                                                                                                                                                                                                                |                                                                                                                                                         cGATATACCTTTTGCCCTAATATTTTTTGTCGATATTTACTGGTGATACGATAGCATTCGTTTTTAATGTCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCAttttttgtac                                                                                                                               <  1:410405/251‑8 (MQ=255) cGATATACCTTTTGCCCTAATATTTTTTGTCGATATTTACTGGTGATACGATAGCATTCGTTTTTAATGTCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCAttttttgta                                                                                                                                >  1:71111/1‑244 (MQ=255)   atataccttttGCCCTAATATTTTTTGTCGATATTTACTGGTGATACGATAGCATTCGTTTTTAATGTCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCAttttttgtactt                                                                                                                             >  1:877799/8‑242 (MQ=255)        ccttttGCCCTAATATTTTTTGTCGATATTTACTGGTGATACGATAGCATTCGTTTTTAATGTCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCAttttttgtacttctgat                                                                                                                        <  1:163853/249‑15 (MQ=255)                                   aTTTACTGGTGATACGATAGCATTCGTTTTTAATGTCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCAttttttgtacttctgattttgtgg                                                                                                                 >  1:761182/1‑210 (MQ=255)                                                                     gTCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCa                                                           >  1:332126/1‑251 (MQ=255)                                                                      tCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCa                                                           <  1:173188/250‑1 (MQ=255)                                                                      tCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCa                                                           <  1:874140/250‑1 (MQ=255)                                                                      tCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCa                                                           <  1:53841/250‑1 (MQ=255)                                                                              aaCCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTa                                                  <  1:617744/251‑1 (MQ=255)                                                                               aCCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaa                                                 >  1:185175/1‑250 (MQ=255)                                                                                    aGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaagctc                                             <  1:459109/250‑6 (MQ=255)                                                                                     gATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCa                                                           <  1:205277/235‑1 (MQ=255)                                                                                      aTTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaagctc                                             <  1:118435/248‑6 (MQ=255)                                                                                         gTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCAttttttgtacttctgatt                                                                                                                       >  1:126125/1‑156 (MQ=255)                                                                                         gTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaagctcactaca                                       >  1:801555/1‑240 (MQ=255)                                                                                         gTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaagctcactaca                                       >  1:271261/1‑240 (MQ=255)                                                                                         gTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTa                                                  <  1:830119/240‑1 (MQ=255)                                                                                           tCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTGCCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaagctcactacaaa                                     >  1:640863/1‑238 (MQ=255)                                                                                           tCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaagctcactac                                        <  1:495319/248‑11 (MQ=255)                                                                                             ccATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaagctcactacaaaac                                   <  1:89452/251‑16 (MQ=255)                                                                                                           ttGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTAAGCTCACTACAAAACTAAtaaggagagac                     <  1:397716/251‑11 (MQ=255)                                                                                                                 tAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTAAGCTCACTACAAAACTAAtaaggagagactgccat               >  1:213856/1‑235 (MQ=255)                                                                                                                      aTCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaagc                                               <  1:806579/214‑4 (MQ=255)                                                                                                                       tCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTAAGCTCACTACAAAACTAAtaaggagagactgccatatttt          >  1:37004/1‑229 (MQ=255)                                                                                                                       tCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTAAGCTCACTACAAAACTAAtaaggagagactgccatatttt          >  1:30421/1‑229 (MQ=255)                                                                                                                             cGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTAAGCTCACTACAAAACTAAtaaggag                         <  1:665929/229‑7 (MQ=255)                                                                                                                             cGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTAAGCTCACTACAAAACTAAT‑AAGGAGAGACTGCCATATTTTCGGATaa  >  1:637904/1‑251 (MQ=255)                                                                                                                             cGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTAAGCTCACTACAAAACTAAT‑AAGGAGAGACTGCCATATTTTCGGATaa  >  1:561656/1‑251 (MQ=255)                                                                                                                              gCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTtttttcttc                                                                                                                                                    >  1:381531/1‑105 (MQ=255)                                                                                                                              gCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaagctcac                                           <  1:703339/210‑8 (MQ=255)                                                                                                                              gCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTAAGCTCACTACAAAACTAAtaagg                           <  1:689161/226‑5 (MQ=255)                                                                                                                                 tttACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaa                                                 >  1:783674/1‑200 (MQ=255)                                                                                                                                        ccccGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTCTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaa                                                 >  1:643501/1‑193 (MQ=255)                                                                                                                                                                                                                                |                                                                                                                                                         CGATAGACTTTTTGCCCCAATATTTTTTGACGGTATTTACTGGTGATACGATAGCATTCGTTTTTAATGTCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACGAATTGCGCACCGATAAAGCGTAAAAGTTTTTTGCCGAGCTTGCCGACGATAATGCCGTTTTCTTCTTCCATCAAGCCCATTTCCCGCGCTTCCGAGGCAGTCGCAAATTCGGCGTTACCATAAAGATTCTTTTTAGGCTGATAGAAGAGTTTCAGCATAATCAGTAGGCAGACGACAAAACTAATCAATAAG‑GATTGCCAGATTTTCGGATAA  >  1/1135164‑1135538

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑