Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,457,239	T→A	V288D (GTT→GAT)	gspD →	Type II secretion system protein GspD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,457,239	0	T	A	100.0%	106.0 / NA	30	V288D (GTT→GAT)	gspD	Type II secretion system protein GspD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (13/17);  total (13/17)

AGAGCGAGGAAGGAAATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGTTTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCTCTTCTGGCGCGATGGATAACGTCGCCATT  >  NC_000913/3457161‑3457315                                                                               |                                                                             agagCGAGGAAGGAAATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGatt                                                                            >  2:658268/1‑81 (MQ=255)      gAGGAAGGAAATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGa                                                                        >  2:658271/1‑80 (MQ=255)       aggaaggaAATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGaaa                                                                      <  1:658228/81‑1 (MQ=255)       aggaaggaAATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGaa                                                                       >  1:658279/1‑80 (MQ=255)        ggaaggaaATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGaaaa                                                                     <  2:658229/81‑1 (MQ=255)        ggaaggaaATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGaa                                                                       >  2:658273/1‑79 (MQ=255)         gaaggaaATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAg                                                                    >  1:658262/1‑81 (MQ=255)           aggaaATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCt                                                                  <  1:658230/81‑1 (MQ=255)            ggaaATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCt                                                                  >  1:658263/1‑80 (MQ=255)             gaaATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTg                                                                 >  2:658277/1‑80 (MQ=255)             gaaATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTg                                                                 >  1:658281/1‑80 (MQ=255)                     cGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGaa                                                        <  1:658231/81‑1 (MQ=255)                           tattaCCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAgg                                                   >  2:658284/1‑80 (MQ=255)                            attaCCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAggg                                                  <  2:658232/80‑1 (MQ=255)                                ccTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATgc                                             >  2:658272/1‑81 (MQ=255)                                   gAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGcgcg                                          >  1:658278/1‑81 (MQ=255)                                    aaaTATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATgcgc                                           <  2:658234/79‑1 (MQ=255)                                    aaaTATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGt                                         <  2:658233/81‑1 (MQ=255)                                    aaaTATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGt                                         <  1:658235/81‑1 (MQ=255)                                         tGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGcc                                    <  2:658236/81‑1 (MQ=255)                                             aaaGCCACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCcctcc                                >  1:658286/1‑81 (MQ=255)                                                  cACGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCtcttc                           >  2:658237/1‑81 (MQ=255)                                                   aCGAATCTGGTGGAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCtcttct                          <  1:658238/81‑1 (MQ=255)                                                            gtggAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCTCTTCTGGCGCGa                   <  2:658239/79‑1 (MQ=255)                                                            gtggAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCTCTTCTGGCGCGATg                 <  1:658240/81‑1 (MQ=255)                                                             tggAAGTGCTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCTCTTCTGGCGCGATgg                <  1:658241/81‑1 (MQ=255)                                                                     cTAACCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCTCTTCTGGCGCGATGGATAACGTc        <  2:658242/81‑1 (MQ=255)                                                                       aaCCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCTCTTCTGGCGCGATGGATAACGTCGc      >  2:658291/1‑81 (MQ=255)                                                                        aCCGGTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCTCTTCTGGCGCGATGGATAACGTCGcc     <  1:658243/81‑1 (MQ=255)                                                                           ggTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCTCTTCTGGCGCGATGGATAACGTCGCCAtt  <  2:658245/81‑1 (MQ=255)                                                                           ggTGATTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCTCTTCTGGCGCGATGGATAACGTCGCCAtt  <  2:658244/81‑1 (MQ=255)                                                                               |                                                                             AGAGCGAGGAAGGAAATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGTTTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCCTCTTCTGGCGCGATGGATAACGTCGCCATT  >  NC_000913/3457161‑3457315

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑