Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,454,040	A→G	G453G (GGT→GGC)	gspA ←	Type II secretion system protein GspA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,454,040	0	A	G	100.0%	160.2 / NA	46	G453G (GGT→GGC)	gspA	Type II secretion system protein GspA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (27/19);  total (27/19)

GCGGCGATATAGAATTCAAACATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACACCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCCAGAGAATCTCTTCCT  >  NC_000913/3453905‑3454176                                                                                                                                        |                                                                                                                                         gcggcgATATAGAATTCAAACATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGt                                                                                                                                      <  2:644988/140‑1 (MQ=255)  cggcgATATAGAATTCAAACATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTc                                                                                                                                     >  2:277693/1‑140 (MQ=255)    gcgATATAGAATTCAAACATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAg                                                                                                                                   <  1:754925/140‑1 (MQ=255)       atatAGAATTCAAACATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGttt                                                                                                                                <  1:54707/140‑1 (MQ=255)        tataGAATTCAAACATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGtttt                                                                                                                               <  2:98500/140‑1 (MQ=255)        tataGAATTCAAACATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGtttt                                                                                                                               <  1:604394/140‑1 (MQ=255)         ataGAATTCAAACATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTc                                                                                                                              >  2:523019/1‑140 (MQ=255)               ttCAAACATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAgtgg                                                                                                                        <  1:121823/140‑1 (MQ=255)               ttCAAACATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAgtgg                                                                                                                        >  1:503750/1‑140 (MQ=255)                    aCATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCt                                                                                                                   >  1:149885/1‑140 (MQ=255)                                 ccTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGc                                                                                                      >  2:58217/1‑140 (MQ=255)                                  cTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCt                                                                                                     <  2:149885/140‑1 (MQ=255)                                    tCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCttt                                                                                                   <  2:458044/140‑1 (MQ=255)                                          ttgttTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGCGGCTTTTTTGAAATTGCTTTAttttt                                                                                             >  2:345635/1‑140 (MQ=255)                                             tttCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCt                                                                                          <  2:680402/140‑1 (MQ=255)                                               tCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCTCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTAc                                                                                        >  1:21272/1‑140 (MQ=255)                                               tCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTAc                                                                                        >  1:439720/1‑140 (MQ=255)                                               tCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTAc                                                                                        >  2:221828/1‑140 (MQ=255)                                                  ggggAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACcaa                                                                                     >  1:728899/1‑140 (MQ=255)                                                    ggAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACcaaca                                                                                   <  2:428577/140‑1 (MQ=255)                                                      aaaTATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAg                                                                                 <  1:347688/140‑1 (MQ=255)                                                         tatTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGa                                                                              <  2:439720/140‑1 (MQ=255)                                                                ttCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCAc                                                                        <  1:278374/139‑1 (MQ=255)                                                                ttCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCAc                                                                        >  2:278374/1‑139 (MQ=255)                                                                               gTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGtt                                                           >  1:211603/1‑137 (MQ=255)                                                                               gTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGtt                                                           <  2:211603/137‑1 (MQ=255)                                                                               gTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTg                                                        <  2:470096/140‑1 (MQ=255)                                                                                   gCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGa                                                    >  2:681407/1‑140 (MQ=255)                                                                                   gCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGa                                                    >  2:739909/1‑140 (MQ=255)                                                                                    cgctctCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGaa                                                   <  1:628465/138‑1 (MQ=255)                                                                                       tctcCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAata                                                >  2:4722/1‑140 (MQ=255)                                                                                        ctcCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAatat                                               >  1:344443/1‑140 (MQ=255)                                                                                         tcCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATg                                              >  1:86006/1‑140 (MQ=255)                                                                                                ccacctgccaGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCCCTCCGCCGAAGGTTCTGTCGAAATATGCAATgcg                                       <  2:21272/140‑1 (MQ=255)                                                                                                ccacctgccaGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATgcg                                       <  1:221828/140‑1 (MQ=255)                                                                                                ccacctgccaGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATgcg                                       >  2:447131/1‑140 (MQ=255)                                                                                                     tgccaGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGtt                                  >  1:334540/1‑140 (MQ=255)                                                                                                     tgccaGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGtt                                  >  2:445089/1‑140 (MQ=255)                                                                                                       ccaGAGATGTACTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTa                                <  1:523019/140‑1 (MQ=255)                                                                                                                  cTAACGTTGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGCGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTcc                     <  1:345635/140‑1 (MQ=255)                                                                                                                        ttGAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTccagccag               >  1:356449/1‑140 (MQ=255)                                                                                                                          gAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCCagag             >  1:739146/1‑140 (MQ=255)                                                                                                                          gAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCCagag             >  2:467762/1‑140 (MQ=255)                                                                                                                          gAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCCagag             >  2:390581/1‑140 (MQ=255)                                                                                                                          gAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCCagag             >  2:216072/1‑140 (MQ=255)                                                                                                                          gAAAAGCCAACAACGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCAagag             >  2:435804/1‑140 (MQ=255)                                                                                                                                 caacaaCGCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCCAGAGAATctct      >  1:353667/1‑140 (MQ=255)                                                                                                                                     aacgCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCCAGAGAATCTCTTCCt  <  2:462058/140‑1 (MQ=255)                                                                                                                                     aacgCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCCAGAGAATCTCTTCCt  <  1:277693/140‑1 (MQ=255)                                                                                                                                     aacgCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCCAGAGAATCTCTTCCt  <  1:467762/140‑1 (MQ=255)                                                                                                                                     aacgCCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCCAGAGAATCTCTTCCt  <  1:390581/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                         GCGGCGATATAGAATTCAAACATGTCATTTCCCCTTCACTGTTGTTTCCGGGGAAATATTTGCTTCATCCCGATATAAGTAGGCACTCTCCCCTGCCACCTGCCAGAGATGTACTAACGTTGAAAAGCCAACAACACCGTCAGTTTTCAAGTGGTGGCTTTTTTGAAATTGCTTTATTTTTTCTACCAACAAGGGACGCCACTCCGCCGAAGGTTCTGTCGAAATATGCAATGCGCGGTTTAACATCGTTTCCAGCCAGAGAATCTCTTCCT  >  NC_000913/3453905‑3454176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑