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%	124.3 / NA	37	E369G (GAA→GGA)	gspL	type II secretion system protein GspL
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (16/21);  total (16/21)

TCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGA  >  NZ_CP009273/3458304‑3458463                                                                                   |                                                                              tCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACa                                                                        <  2:65379/90‑1 (MQ=255)  cGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAg                                                                       >  1:383865/1‑90 (MQ=255)           tAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                              <  1:212836/90‑1 (MQ=255)           tAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                              <  2:161579/90‑1 (MQ=255)             aaaaTGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCg                                                            <  1:65069/90‑1 (MQ=255)                aTGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                         >  1:230007/1‑90 (MQ=255)                  gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                       <  2:419876/90‑1 (MQ=255)                    gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                     <  2:363422/90‑1 (MQ=255)                    gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                     <  1:311563/90‑1 (MQ=255)                    gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                     <  1:321989/90‑1 (MQ=255)                    gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                     <  2:79789/90‑1 (MQ=255)                              tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                         <  1:182015/76‑1 (MQ=255)                              tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                         >  2:182015/1‑76 (MQ=255)                              tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                           >  2:411046/1‑90 (MQ=255)                              tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                           >  2:291205/1‑90 (MQ=255)                              tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                           <  2:96849/90‑1 (MQ=255)                              tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                           <  2:230007/90‑1 (MQ=255)                              tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                           <  1:123665/90‑1 (MQ=255)                              tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                           <  1:242971/90‑1 (MQ=255)                              tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                           <  1:204334/90‑1 (MQ=255)                                aaGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAg                                         >  1:70337/1‑90 (MQ=255)                                     aaTATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAgg                                    <  2:70337/90‑1 (MQ=255)                                     aaTATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAgg                                    >  1:157465/1‑90 (MQ=255)                                           gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                         <  2:168749/63‑1 (MQ=255)                                           gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                         >  1:168749/1‑63 (MQ=255)                                           gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGGGTATGGACAGTAAGGAACTCa                              >  1:365486/1‑90 (MQ=255)                                            atcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAg                             >  1:126362/1‑90 (MQ=255)                                            atcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAg                             >  2:356002/1‑90 (MQ=255)                                                 ttCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGaaa                        <  2:362393/90‑1 (MQ=255)                                                               acaGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtgg          <  1:33672/90‑1 (MQ=255)                                                                  gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGaaa                        >  2:243427/1‑73 (MQ=255)                                                                  gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGaaa                        <  1:243427/73‑1 (MQ=255)                                                                  gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtgg       >  2:278219/1‑90 (MQ=255)                                                                  gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtgg       >  1:272525/1‑90 (MQ=255)                                                                       ggCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGa  >  1:110132/1‑90 (MQ=255)                                                                            ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                           <  1:144526/44‑1 (MQ=255)                                                                            ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                           >  2:144526/1‑44 (MQ=255)                                                                                   |                                                                              TCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGA  >  NZ_CP009273/3458304‑3458463

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑