Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,459,753	T→C	I472T (ATA→ACA)	gspE →	Type II secretion system protein GspE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,459,753	0	T	C	100.0%	170.5 / NA	49	I472T (ATA→ACA)	gspE	Type II secretion system protein GspE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (21/28);  total (21/28)

ATGTGGATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGATAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATTATCGCTA  >  NC_000913/3459675‑3459830                                                                               |                                                                              aTGTGGATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACaa                                                                             <  1:658843/81‑1 (MQ=255) aTGTGGATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACaa                                                                             <  2:658844/81‑1 (MQ=255)    tgGATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGc                                                                           <  1:658845/80‑1 (MQ=255)    tgGATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCg                                                                          <  1:658846/81‑1 (MQ=255)      gATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCgg                                                                         <  2:658847/80‑1 (MQ=255)       aTGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTg                                                                       <  2:658848/81‑1 (MQ=255)          aaCAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGaca                                                                    >  2:658891/1‑81 (MQ=255)             aaGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACAcct                                                                 <  1:658849/81‑1 (MQ=255)             aaGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACAcct                                                                 <  1:658850/81‑1 (MQ=255)              aGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACAcctc                                                                >  2:658915/1‑81 (MQ=255)               gCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACAcctcc                                                               >  2:658903/1‑81 (MQ=255)                  cTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTgg                                                            <  2:658851/81‑1 (MQ=255)                    ggAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGa                                                          >  2:658902/1‑81 (MQ=255)                    ggAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGa                                                          >  2:658913/1‑81 (MQ=255)                     gAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTggg                                                           <  2:658853/79‑1 (MQ=255)                     gAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTggg                                                           <  2:658852/79‑1 (MQ=255)                       gCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGAt                                                         >  1:658906/1‑79 (MQ=255)                         gACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAgg                                                     >  1:658886/1‑81 (MQ=255)                         gACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAgg                                                     >  1:658899/1‑81 (MQ=255)                           cTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGtt                                                   <  2:658854/81‑1 (MQ=255)                            tAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTa                                                  >  1:658921/1‑81 (MQ=255)                              gTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATg                                                >  1:658919/1‑81 (MQ=255)                               tCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATgc                                               <  1:658855/81‑1 (MQ=255)                                 cGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATgcgc                                             <  2:658856/81‑1 (MQ=255)                                    caacaaCACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTc                                          >  2:658918/1‑81 (MQ=255)                                    caacaaCACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTc                                          >  2:658898/1‑81 (MQ=255)                                     aacaacACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCg                                         >  1:658917/1‑81 (MQ=255)                                       caacaCAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGcc                                       <  2:658857/81‑1 (MQ=255)                                        aacaCAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCa                                      <  1:658858/81‑1 (MQ=255)                                          cacaAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGt                                    >  2:658923/1‑81 (MQ=255)                                              aGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCa                                <  2:658859/81‑1 (MQ=255)                                               ggCCTTAATCAAAAATGGCCTGCAAAAAGTGGCAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCAc                               <  1:658860/81‑1 (MQ=255)                                                gCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACg                              <  2:658861/81‑1 (MQ=255)                                                 ccTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGc                             <  1:658862/81‑1 (MQ=255)                                                    tAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTg                           >  1:658929/1‑80 (MQ=255)                                                     aaTCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTg                           >  2:658911/1‑79 (MQ=255)                                                         aaaaaTGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGagag                      <  1:658863/80‑1 (MQ=255)                                                            aaTGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGaa                  <  1:658864/81‑1 (MQ=255)                                                               ggCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCa               >  1:658910/1‑81 (MQ=255)                                                                     cAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAAtt         <  2:658865/81‑1 (MQ=255)                                                                     cAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAAt          >  2:658905/1‑80 (MQ=255)                                                                      aaaaaGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATta        <  1:658866/81‑1 (MQ=255)                                                                      aaaaaGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATta        >  2:658925/1‑81 (MQ=255)                                                                        aaaGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATtatc      >  2:658887/1‑81 (MQ=255)                                                                        aaaGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATtatc      <  2:658867/81‑1 (MQ=255)                                                                          aGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATtatcgc    <  2:658868/81‑1 (MQ=255)                                                                           gTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATtatcgct   <  2:658869/81‑1 (MQ=255)                                                                           gTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATtatcgc    >  2:658916/1‑80 (MQ=255)                                                                            tGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATtatcgcta  <  1:658870/81‑1 (MQ=255)                                                                               |                                                                              ATGTGGATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGATAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATTATCGCTA  >  NC_000913/3459675‑3459830

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑