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%	166.3 / NA	46	E369G (GAA→GGA)	gspL	type II secretion system protein GspL
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (28/18);  total (28/18)

TCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATC  >  NZ_CP009273/3458304‑3458469                                                                                     |                                                                                    tCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACa                                                                              <  2:648668/90‑1 (MQ=255) tCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACa                                                                              >  1:451955/1‑90 (MQ=255)  cGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAg                                                                             >  1:702818/1‑90 (MQ=255)    cTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGaa                                                                           >  2:98758/1‑90 (MQ=255)           tAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                                    <  1:327660/90‑1 (MQ=255)           tAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                                    <  2:236597/90‑1 (MQ=255)                aTGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                               <  1:467796/90‑1 (MQ=255)                  gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                             <  2:553738/90‑1 (MQ=255)                  gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                             >  2:525187/1‑90 (MQ=255)                  gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                             >  2:24683/1‑90 (MQ=255)                    gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                           <  2:406076/90‑1 (MQ=255)                         aaGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTa                                                      <  2:102432/90‑1 (MQ=255)                              tGAAGCTAATATCGATCGTTTCTGTGAGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATgg                                                   >  2:369772/1‑90 (MQ=255)                              tGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                 <  1:104509/90‑1 (MQ=255)                                aaGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                               >  1:188970/1‑74 (MQ=255)                                aaGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                               <  2:188970/74‑1 (MQ=255)                                     aaTATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAgg                                          >  2:305835/1‑90 (MQ=255)                                     aaTATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAgg                                          <  2:410729/90‑1 (MQ=255)                                     aaTATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAgg                                          >  2:448512/1‑90 (MQ=255)                                          cgatcgTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTc                                     <  2:340916/90‑1 (MQ=255)                                            atcgTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                               <  2:229966/62‑1 (MQ=255)                                            atcgTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTc                                                               >  1:229966/1‑62 (MQ=255)                                            atcgTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAg                                   >  2:664457/1‑90 (MQ=255)                                                 ttCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGaaa                              >  1:240636/1‑90 (MQ=255)                                                 ttCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGaaa                              <  2:499941/90‑1 (MQ=255)                                                         gAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                 <  1:705215/65‑1 (MQ=255)                                                         gAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                 >  2:705215/1‑65 (MQ=255)                                                            ttAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAAt                     <  1:462891/90‑1 (MQ=255)                                                            ttAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAAt                     <  1:388342/90‑1 (MQ=255)                                                             tAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATc                    >  1:557072/1‑90 (MQ=255)                                                                   aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtg              >  2:221782/1‑90 (MQ=255)                                                                   aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtg              >  1:118740/1‑90 (MQ=255)                                                                   aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtg              >  2:65584/1‑90 (MQ=255)                                                                   aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtg              >  2:447689/1‑90 (MQ=255)                                                                   aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtg              >  2:418646/1‑90 (MQ=255)                                                                   aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtg              >  1:407832/1‑90 (MQ=255)                                                                   aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtg              >  2:266994/1‑90 (MQ=255)                                                                   aGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtg              >  2:24809/1‑90 (MQ=255)                                                                     tCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTggg            >  1:524707/1‑90 (MQ=255)                                                                         ggCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGa        >  1:501331/1‑90 (MQ=255)                                                                              ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAg                                               >  1:247961/1‑46 (MQ=255)                                                                              ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAg                                               <  2:247961/46‑1 (MQ=255)                                                                              ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt   >  1:244591/1‑90 (MQ=255)                                                                              ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt   >  2:613609/1‑90 (MQ=255)                                                                              ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt   >  2:143981/1‑90 (MQ=255)                                                                               cGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATc  <  1:369772/90‑1 (MQ=255)                                                                                     |                                                                                    TCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGT‑‑GAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATC  >  NZ_CP009273/3458304‑3458469

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: ‑