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%	136.7 / NA	39	I472T (ATA→ACA)	gspE	Type II secretion system protein GspE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/19);  total (20/19)

TGTGGATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGATAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATTATCGCTA  >  NC_000913/3459676‑3459830                                                                              |                                                                              tgtgGATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAg                                                                            >  1:594068/1‑81 (MQ=255)   tgGATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGc                                                                           <  1:594034/80‑1 (MQ=255)    ggATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCgg                                                                         >  2:594081/1‑81 (MQ=255)     gATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGt                                                                        >  1:594090/1‑81 (MQ=255)           cAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACAcc                                                                  >  1:594087/1‑81 (MQ=255)            aaGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACAcct                                                                 >  2:594084/1‑81 (MQ=255)            aaGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACAcct                                                                 >  2:594071/1‑81 (MQ=255)             aGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACAcctc                                                                >  2:594073/1‑81 (MQ=255)              gCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACAcctcc                                                               <  1:594035/81‑1 (MQ=255)              gCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACAcctcc                                                               >  1:594100/1‑81 (MQ=255)                     aGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGAt                                                         >  2:594092/1‑80 (MQ=255)                     aGCGACTAGTCCGGCAACAACACAAAGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATg                                                        <  2:594035/81‑1 (MQ=255)                      gCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGa                                                       <  1:594037/81‑1 (MQ=255)                          cTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGtt                                                   <  1:594038/81‑1 (MQ=255)                            aGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTAt                                                 >  2:594078/1‑81 (MQ=255)                               ccGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATgcg                                              >  1:594081/1‑81 (MQ=255)                                cGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATgcgc                                             >  1:594092/1‑81 (MQ=255)                                cGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATgcgc                                             >  1:594096/1‑81 (MQ=255)                                 ggCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGcgcg                                            <  2:594038/81‑1 (MQ=255)                                   caacaaCACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTc                                          <  1:594040/81‑1 (MQ=255)                                    aacaacACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCg                                         >  2:594103/1‑81 (MQ=255)                                      caacaCAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGcc                                       <  1:594041/81‑1 (MQ=255)                                         cacaAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGt                                    >  2:594079/1‑81 (MQ=255)                                            aaGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGc                                  >  2:594111/1‑80 (MQ=255)                                             aGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCa                                >  2:594093/1‑81 (MQ=255)                                             aGGCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCa                                <  2:594041/81‑1 (MQ=255)                                               gCCTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACg                              <  1:594043/81‑1 (MQ=255)                                                 cTTAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCt                            <  1:594044/81‑1 (MQ=255)                                                   tAATCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTg                           >  2:594101/1‑80 (MQ=255)                                                     aTCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGgag                        <  2:594044/81‑1 (MQ=255)                                                      tCAAAAATGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGgaga                       <  1:594046/81‑1 (MQ=255)                                                         aaaaTGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGc                     >  2:594085/1‑80 (MQ=255)                                                          aaaTGGCCTGCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGa                   <  2:594046/81‑1 (MQ=255)                                                                   gCAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAAt          >  1:594106/1‑81 (MQ=255)                                                                    cAAAAAGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAAtt         <  2:594047/81‑1 (MQ=255)                                                                      aaaaGTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATtat       <  2:594048/81‑1 (MQ=255)                                                                          gTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATtatcgct   <  1:594050/81‑1 (MQ=255)                                                                          gTGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATtatcgct   <  1:594051/81‑1 (MQ=255)                                                                           tGACAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATtatcgcta  <  2:594051/81‑1 (MQ=255)                                                                              |                                                                              TGTGGATGAACAAGCACTGGAGCGACTAGTCCGGCAACAACACAAGGCCTTAATCAAAAATGGCCTGCAAAAAGTGATAAGCGGTGACACCTCCTGGGATGAGGTTATGCGCGTCGCCAGTGCCACGCTGGAGAGCGAAGCATGAATTATCGCTA  >  NC_000913/3459676‑3459830

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑