Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,463,048	A→C	N42T (AAC→ACC)	gspK →	Type II secretion system protein GspK

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,463,048	0	A	C	100.0%	167.9 / NA	47	N42T (AAC→ACC)	gspK	Type II secretion system protein GspK
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (24/23);  total (24/23)

CCATGAATAATGAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAAACC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTGCAGCAGTACTGGGCACAGCCACAACAGT  >  NC_000913/3462922‑3463176                                                                                                                               |                                                                                                                                  ccATGAATAATGAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCc‑atca                                                                                                                            >  2:83642/1‑133 (MQ=255)  cATGAATAATGAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCc‑atcat                                                                                                                           >  2:597547/1‑133 (MQ=255)   aTGAATAATGAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑atcatc                                                                                                                          >  2:497332/1‑133 (MQ=255)   aTGAATAATGAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑atcatc                                                                                                                          >  1:564215/1‑133 (MQ=255)    tGAATAATGAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCt                                                                                                                         >  1:122728/1‑133 (MQ=255)      aataatGAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGc                                                                                                                       >  2:529912/1‑133 (MQ=255)        taatGAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCaa                                                                                                                     <  1:497332/133‑1 (MQ=255)           tGAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACgg                                                                                                                  <  2:320873/133‑1 (MQ=255)           tGAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACgg                                                                                                                  <  2:564215/133‑1 (MQ=255)            gAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGc                                                                                                                 >  2:581508/1‑133 (MQ=255)             aacaacGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCa                                                                                                                <  1:581508/133‑1 (MQ=255)               caacGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGTCAGATAACCC‑ATAATCTTAAACGGCact                                                                                                              >  2:302489/1‑131 (MQ=255)                aacGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCtata                                                                                                             <  1:597547/133‑1 (MQ=255)                  cgcgGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTTAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATg                                                                                                           >  2:534154/1‑133 (MQ=255)                  cgcgGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCaa                                                                                                                     <  1:270781/123‑1 (MQ=255)                  cgcgGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCaa                                                                                                                     >  2:270781/1‑123 (MQ=255)                    cggcgTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAAGTAACCC‑CTCAGCTGCAACGGCAATATGat                                                                                                         >  1:213957/1‑133 (MQ=255)                     ggcgTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGata                                                                                                        >  2:584250/1‑133 (MQ=255)                     ggcgTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGata                                                                                                        >  1:342966/1‑133 (MQ=255)                                       gTACTCATGTAACTGCCGCTCATGGCTGCTCTCGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAAc                                                                                      <  2:287757/133‑1 (MQ=255)                                              tGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCt                                                                               >  1:53292/1‑133 (MQ=255)                                              tGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCt                                                                               >  1:524211/1‑133 (MQ=255)                                              tGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCt                                                                               >  1:620550/1‑133 (MQ=255)                                                  aCTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGcc                                                                           >  2:431491/1‑133 (MQ=255)                                                     ggCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTTAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGc                                                                        <  1:534154/133‑1 (MQ=255)                                                     ggCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGc                                                                        <  2:620550/133‑1 (MQ=255)                                                     ggCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGc                                                                        <  2:122728/133‑1 (MQ=255)                                                         cTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCa                                                                    >  2:482879/1‑133 (MQ=255)                                                           cATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCAcc                                                                  >  2:105388/1‑133 (MQ=255)                                                             tGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCa                                                                <  2:624953/133‑1 (MQ=255)                                                              ggCTGCTCTGGCAGCGGACATGACGCTCTGTTATCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAg                                                               <  2:213957/133‑1 (MQ=255)                                                                  gctCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACg                                                           <  2:30291/133‑1 (MQ=255)                                                                         cagcagACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGa                                                    <  1:83642/133‑1 (MQ=255)                                                                                cATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACgac                                             <  1:431491/133‑1 (MQ=255)                                                                                          aGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCa                                   >  2:460224/1‑133 (MQ=255)                                                                                          aGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCa                                   <  2:524211/133‑1 (MQ=255)                                                                                           gTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCAc                                  >  2:594951/1‑133 (MQ=255)                                                                                               tCACAGCCAGCTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTg                              <  1:105388/133‑1 (MQ=255)                                                                                                  ccgccaggTTTAACGGAACCGCCAGGTAACCC‑ATCATCTGGAACGGCAATTTGAAATTGAACCGGCGGAGAAACTTGGGCTTGCCAGCCCCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTgcag                           <  2:136824/131‑1 (MQ=255)                                                                                                  cagccagcTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTgcag                           <  2:53292/133‑1 (MQ=255)                                                                                                  cagccagcTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTgcag                           <  2:557622/133‑1 (MQ=255)                                                                                                  cagccagcTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTgcag                           <  2:103105/133‑1 (MQ=255)                                                                                                  cagccagcTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTgcag                           <  1:529912/133‑1 (MQ=255)                                                                                                    gccagcTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCACCCCCCCCCAGACCGTTAAAGTTAACGCAAGACGAACCAGGTTgcaccg                         >  1:491817/1‑130 (MQ=255)                                                                                                    accaacTTCAGCCAACCCCGCAGGTAACCCAACCACCTCAACCGGCAAAATAATATTAACCTGG‑GGGGGAACTTGCCCTTTGCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTgcagca                         <  2:491817/132‑1 (MQ=255)                                                                                                      cagcTTCAGCGAACCCGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTGCAGCAGt                       >  2:3486/1‑133 (MQ=255)                                                                                                                   cccGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTGCAGCAGTACTGGGCACAGcc          <  1:482879/133‑1 (MQ=255)                                                                                                                     cGCCAGGTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTGCAGCAGTACTGGGCACAGCcac        <  1:584250/133‑1 (MQ=255)                                                                                                                           gTAACCC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGGTGCAGCAGTACGGGACACAGCGACAACAGt  >  1:169912/1‑133 (MQ=255)                                                                                                                               |                                                                                                                                  CCATGAATAATGAACAACGCGGCGTCGCGCTGCTCATTGTACTCATGTTACTGGCGCTCATGGCTGCTCTGGCAGCAGACATGACGCTCAGTTTTCACAGCCAGCTTCAGCGAACCCGCCAGGTAAACC‑ATCATCTGCAACGGCAATATGATATTGAACTGGCGGAGAAACTTGCGCTTGCCAGCCTCACCCAGGACGTTAAAGATAACGACAGACAGACCACGTTGCAGCAGTACTGGGCACAGCCACAACAGT  >  NC_000913/3462922‑3463176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑