Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,459,938	T→C	I41T (ATT→ACT)	gspF →	Type II secretion system protein GspF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,459,938	0	T	C	100.0%	163.3 / NA	45	I41T (ATT→ACT)	gspF	Type II secretion system protein GspF
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (24/21);  total (24/21)

GCAAGGGATCATTGATGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATATTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGAACTGACGCTTTTCACCCG  >  NC_000913/3459861‑3460013                                                                              |                                                                            gCAAGGGATCATTGATGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCg                                                                          >  2:651696/1‑81 (MQ=255) gCAAGGGATCATTGATGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCg                                                                          >  1:651700/1‑81 (MQ=255) gCAAGGGATCATTGATGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCg                                                                          >  1:651698/1‑81 (MQ=255)   aaGGGATCATTGATGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGcc                                                                        <  1:651651/81‑1 (MQ=255)    aGGGATCATTGATGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGccc                                                                       <  1:651652/81‑1 (MQ=255)       gATCATTGATGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGccccc                                                                     >  2:651704/1‑80 (MQ=255)        aTCATTGATGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCaa                                                                   <  1:651653/81‑1 (MQ=255)        aTCATTGATGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCaa                                                                   <  2:651654/81‑1 (MQ=255)              gATGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGt                                                             >  1:651699/1‑81 (MQ=255)               aTGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGt                                                             <  1:651655/80‑1 (MQ=255)                 gCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCg                                                          >  1:651695/1‑81 (MQ=255)                     aCGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCggg                                                        <  2:651656/79‑1 (MQ=255)                      cGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAg                                                      >  2:651702/1‑80 (MQ=255)                       gATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTa                                                    <  1:651657/81‑1 (MQ=255)                        aTGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTaa                                                   <  1:651658/81‑1 (MQ=255)                        aTGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTaa                                                   <  2:651659/81‑1 (MQ=255)                         tGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTaaa                                                  <  1:651660/81‑1 (MQ=255)                           aaCGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTaaaaa                                                >  2:651727/1‑81 (MQ=255)                             cGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAaca                                              <  1:651661/81‑1 (MQ=255)                                cAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGt                                           >  2:651716/1‑81 (MQ=255)                                 aGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTc                                          <  2:651662/81‑1 (MQ=255)                                   gCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGc                                        >  1:651718/1‑81 (MQ=255)                                     aCGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGccc                                      >  2:651711/1‑81 (MQ=255)                                     aCGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGccc                                      <  1:651663/81‑1 (MQ=255)                                         cTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAg                                   >  2:651706/1‑80 (MQ=255)                                         cTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAATTCGGGAGTAAAAACACGTCGCCCGAgg                                  <  2:651664/81‑1 (MQ=255)                                            cGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGAt                                <  2:651665/80‑1 (MQ=255)                                             ggCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGAt                                >  2:651729/1‑79 (MQ=255)                                              gCTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAg                             >  2:651717/1‑81 (MQ=255)                                               cTGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGc                            <  1:651666/81‑1 (MQ=255)                                                tGCGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGc                            >  2:651725/1‑80 (MQ=255)                                                  cGTGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCa                          >  1:651722/1‑80 (MQ=255)                                                    tGAAGAAGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAg                       >  1:651708/1‑81 (MQ=255)                                                     gaagaaGGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGt                      >  1:651707/1‑81 (MQ=255)                                                       agaagGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTg                     >  1:651713/1‑80 (MQ=255)                                                        gaagGGCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGaa                   >  1:651724/1‑81 (MQ=255)                                                             gCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGAACTGAc              <  2:651669/81‑1 (MQ=255)                                                             gCTTTTCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGAACTGAc              <  1:651668/81‑1 (MQ=255)                                                             gCTTGTCCTGCTGGATACTCGCCCCCAAAAAGGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGAACTGAc              <  2:651667/81‑1 (MQ=255)                                                                 ttCCTGCTGGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGAACTGACGCtt          >  1:651715/1‑81 (MQ=255)                                                                    ctgctgGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGAACTGACGCtttt        <  2:651670/80‑1 (MQ=255)                                                                       ctgGATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGAACTGACGCTTTTCAcc    >  1:651714/1‑81 (MQ=255)                                                                         ggATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGAACTGACGCTTTTCACCCg  >  2:651712/1‑81 (MQ=255)                                                                         ggATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGAACTGACGCTTTTCACCCg  >  1:651721/1‑81 (MQ=255)                                                                          gATACTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGAACTGACGCTTTTCAccc   <  1:651671/79‑1 (MQ=255)                                                                              |                                                                            GCAAGGGATCATTGATGCTAACGATGAACGTCAGGCACGACTGCGGCTGCGTGAAGAAGGGCTTTTCCTGCTGGATATTCGCCCCCAAAAAAGTTCGGGAGTAAAAACACGTCGCCCGAGGATCAGCCATAGTGAACTGACGCTTTTCACCCG  >  NC_000913/3459861‑3460013

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: ‑