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%	275.8 / NA	78	E369G (GAA→GGA)	gspL	type II secretion system protein GspL
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (42/36);  total (42/36)

AAGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAT  >  NZ_CP009273/3458301‑3458468                                                                                      |                                                                                   aaGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGgaaaa                                                                                <  2:1134722/90‑1 (MQ=255)      gCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGa                                                                           >  2:411097/1‑90 (MQ=255)         gACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGaaaa                                                                        <  1:769020/90‑1 (MQ=255)              tAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                                   <  1:50485/90‑1 (MQ=255)              tAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                                   <  2:675571/90‑1 (MQ=255)                     gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                            >  2:855532/1‑90 (MQ=255)                     gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                            >  2:239085/1‑90 (MQ=255)                     gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                            <  1:209077/90‑1 (MQ=255)                     gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                            >  1:707813/1‑90 (MQ=255)                     gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                            >  2:1145189/1‑90 (MQ=255)                     gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                            >  1:1124542/1‑90 (MQ=255)                     gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                            <  2:792516/90‑1 (MQ=255)                       gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                          <  1:1145189/90‑1 (MQ=255)                       gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                          <  1:771252/90‑1 (MQ=255)                       gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                          <  1:680703/90‑1 (MQ=255)                       gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                          <  1:1085794/90‑1 (MQ=255)                       gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                          <  2:81695/90‑1 (MQ=255)                       gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                          <  2:215379/90‑1 (MQ=255)                       gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                          <  1:1045298/90‑1 (MQ=255)                         gCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtggt                                                        >  1:379033/1‑90 (MQ=255)                               agTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATgg                                                  <  2:379033/90‑1 (MQ=255)                                 tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                <  2:115227/90‑1 (MQ=255)                                 tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                <  1:827858/90‑1 (MQ=255)                                 tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                <  1:239085/90‑1 (MQ=255)                                  gAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                <  1:640375/89‑1 (MQ=255)                                  gAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                >  2:640375/1‑89 (MQ=255)                                   aaGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAg                                              >  1:983939/1‑90 (MQ=255)                                        aaTATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAgg                                         >  2:13772/1‑90 (MQ=255)                                             cgatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTc                                    >  1:337365/1‑90 (MQ=255)                                             cgatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTc                                    <  2:677319/90‑1 (MQ=255)                                              gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                          <  2:1099019/67‑1 (MQ=255)                                              gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                          >  1:1099019/1‑67 (MQ=255)                                              gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                <  2:159803/77‑1 (MQ=255)                                              gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                >  1:159803/1‑77 (MQ=255)                                              gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCa                                   <  1:1093130/90‑1 (MQ=255)                                               atcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAg                                  >  1:257361/1‑90 (MQ=255)                                                  gTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGa                               >  1:132474/1‑90 (MQ=255)                                                    ttCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGaaa                             <  1:532378/90‑1 (MQ=255)                                                    ttCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGaaa                             <  1:1081173/90‑1 (MQ=255)                                                    ttCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGaaa                             <  1:787027/90‑1 (MQ=255)                                                    ttCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGaaa                             <  1:377273/90‑1 (MQ=255)                                                     tCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAAt                            <  1:1225856/90‑1 (MQ=255)                                                        gtgAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGAt                         <  2:707813/90‑1 (MQ=255)                                                        gtgAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGAt                         <  2:257361/90‑1 (MQ=255)                                                            gTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                              >  2:92855/1‑49 (MQ=255)                                                            gTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                              <  1:92855/49‑1 (MQ=255)                                                              tAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATc                   >  2:699628/1‑90 (MQ=255)                                                                  acaGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtgg               <  1:1000425/90‑1 (MQ=255)                                                                    aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                          >  1:1001938/1‑45 (MQ=255)                                                                    aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                          <  2:1001938/45‑1 (MQ=255)                                                                    aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                >  2:636147/1‑55 (MQ=255)                                                                    aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                <  1:636147/55‑1 (MQ=255)                                                                    aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtg             <  2:322624/90‑1 (MQ=255)                                                                    aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtg             >  2:103177/1‑90 (MQ=255)                                                                    aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtg             >  2:1077541/1‑90 (MQ=255)                                                                     gTCCTGGCTTCCGATGGGGAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                >  2:278974/1‑54 (MQ=255)                                                                     gTCCTGGCTTCCGATGGGGAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                <  1:278974/54‑1 (MQ=255)                                                                     gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtgg            >  1:1194995/1‑90 (MQ=255)                                                                     gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtgg            >  2:1137274/1‑90 (MQ=255)                                                                     gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtgg            >  2:346376/1‑90 (MQ=255)                                                                     gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtgg            >  1:893222/1‑90 (MQ=255)                                                                     gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTATATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtgg            >  1:479048/1‑90 (MQ=255)                                                                          ggCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATgg                                                  >  1:1077788/1‑47 (MQ=255)                                                                          ggCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATgg                                                  <  2:1077788/47‑1 (MQ=255)                                                                          ggCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGa       >  2:458480/1‑90 (MQ=255)                                                                          ggCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGa       >  1:264224/1‑90 (MQ=255)                                                                          ggCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGa       >  1:295254/1‑90 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTa                       >  1:70179/1‑69 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt  >  1:710838/1‑90 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt  >  2:565278/1‑90 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt  >  1:34695/1‑90 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt  >  1:226313/1‑90 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt  >  1:587691/1‑90 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt  >  1:199824/1‑90 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt  >  1:597700/1‑90 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt  >  1:761373/1‑90 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt  >  2:1241242/1‑90 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGAACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt  >  2:262062/1‑90 (MQ=255)                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTACGGACAGTAAGGAACTCAGGGAAATGATTa                       <  2:70179/69‑1 (MQ=255)                                                                                      |                                                                                   AAGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAT  >  NZ_CP009273/3458301‑3458468

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: ‑