Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,458,386	A→G	E369G (GAA→GGA)	gspL →	type II secretion system protein GspL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,458,386	0	A	G	100.0%	75.6 / NA	25	E369G (GAA→GGA)	gspL	type II secretion system protein GspL
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (13/12);  total (13/12)

AAAGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCC  >  NZ_CP009273/3458300‑3458470                                                                                       |                                                                                     aaaGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGgaaa                                                                                   <  1:324733/90‑1 (MQ=255)  aaGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGgaaaa                                                                                  <  1:449963/90‑1 (MQ=255)    gTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAAc                                                                                <  1:244401/90‑1 (MQ=255)     tCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACa                                                                               <  1:197359/90‑1 (MQ=255)               tAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                                     <  1:272083/90‑1 (MQ=255)                      gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                              >  1:389824/1‑90 (MQ=255)                      gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                              >  2:203237/1‑90 (MQ=255)                        gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                            <  2:389824/90‑1 (MQ=255)                        gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                            <  2:344222/90‑1 (MQ=255)                                  tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                  <  1:6662/90‑1 (MQ=255)                                  tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                  >  2:2489/1‑90 (MQ=255)                                  tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                  <  2:218543/90‑1 (MQ=255)                                   gAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACa                                                 >  1:25213/1‑90 (MQ=255)                                               gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                                     <  1:390762/58‑1 (MQ=255)                                               gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                                     >  2:390762/1‑58 (MQ=255)                                                atcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAg                                    >  1:251907/1‑90 (MQ=255)                                                 tcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAgg                                           <  1:345145/82‑1 (MQ=255)                                                 tcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAgg                                           >  2:345145/1‑82 (MQ=255)                                                    tttCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGaa                                <  1:305350/90‑1 (MQ=255)                                                                   acaGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtgg                 <  2:25213/90‑1 (MQ=255)                                                                      gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGGTTAAATCAtggtgg              >  2:40034/1‑90 (MQ=255)                                                                      gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtgg              >  1:85052/1‑90 (MQ=255)                                                                           ggCTTCCGATGGGAAAAACAGTGAAAGATCCGGTCAGTGGTGTATGGAc                                                  >  1:411958/1‑49 (MQ=37)                                                                           ggCTTCCGATGGGAAAAACAGAGAAAGATCCGGTCAGTGGTGTATGGAc                                                  <  2:411958/49‑1 (MQ=255)                                                                           ggCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGa         >  2:464575/1‑90 (MQ=255)                                                                                ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt    >  2:311836/1‑90 (MQ=255)                                                                                  gATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATcc  >  1:136401/1‑90 (MQ=255)                                                                                       |                                                                                     AAAGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCC  >  NZ_CP009273/3458300‑3458470

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑