Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,135,418	C→T	S93S (TCG→TCA)	unknown ←	Type IV secretion system protein VirD4

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,135,418	0	C	T	100.0%	67.7 / NA	27	S93S (TCG→TCA)	unknown	Type IV secretion system protein VirD4
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (12/15);  total (12/15)

GTCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACGAATTGCGCACCGATAAAGCGTAAAAGTTTTTTGCCGAGCTTGCCGACGATAATGCCGTTTTCTTCTTCCATCAAGCCCATTTCCCGCGCTTCCGAGGCAGTCGCAAATTCGGCGTTACCATAAAGATTCTTTTTAGGCTGATAGAAGAGTTTCAGCATAATCAGTAGGCAGACGACAAAACTAATCAATAAG‑GATTGCCAGATTTTCGGATAA  >  1/1135232‑1135538                                                                                                                                                                                           |                                                                                                                          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)                     gTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaagctcactaca                                       >  1:271261/1‑240 (MQ=255)                     gTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACAAATTGCGCACCGATAAAACGGAGCAGTTTATTACCGAGTTTGCCGACAATAATCCCGTTTTTTTCTTCCAATAAACCCATTTTTTGTACTTCTGATTTTGTGGCAAATTCAGCGTTACCATAAAGGGATTTTTTAGGTTGATAGAATAGTTTCAGCATGATTAGTaagctcactaca                                       >  1:801555/1‑240 (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)                                                          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)                                                                                                                                                                                           |                                                                                                                          GTCCTTCACAACCACAGATTGTTCCCATGCCAGCAAATTTGGAATAACAATCCCTACGCTTTTACCTCCCCGTGTCGGCGCTGCCAGTGAAACGAATTGCGCACCGATAAAGCGTAAAAGTTTTTTGCCGAGCTTGCCGACGATAATGCCGTTTTCTTCTTCCATCAAGCCCATTTCCCGCGCTTCCGAGGCAGTCGCAAATTCGGCGTTACCATAAAGATTCTTTTTAGGCTGATAGAAGAGTTTCAGCATAATCAGTAGGCAGACGACAAAACTAATCAATAAG‑GATTGCCAGATTTTCGGATAA  >  1/1135232‑1135538

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑