Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,091,305	A→G	S58G (AGC→GGC)	rsmE →	16S rRNA m(3)U1498 methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,091,305	0	A	G	100.0%	350.4 / NA	88	S58G (AGC→GGC)	rsmE	16S rRNA m(3)U1498 methyltransferase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (52/36);  total (52/36)

GTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCAGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATCGACGA  >  NC_000913/3091259‑3091351                                               |                                               gTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGc                                              >  1:5735510/1‑49 (MQ=255) gTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGc                                              <  1:1249756/49‑1 (MQ=255)  tttGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaa                                            <  1:5358384/50‑1 (MQ=255)  tttGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCa                                             <  1:7020454/49‑1 (MQ=255)  tttGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCa                                             <  1:8108180/49‑1 (MQ=255)   ttGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaa                                            >  1:2845631/1‑49 (MQ=255)     gACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaa                                          >  1:543817/1‑49 (MQ=255)     gACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaa                                          >  1:3140335/1‑49 (MQ=255)     gACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaa                                          <  1:1590015/49‑1 (MQ=255)      aCGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaa                                         <  1:903536/49‑1 (MQ=255)      aCGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaa                                         <  1:6783539/49‑1 (MQ=255)       cGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaaaa                                       <  1:1740188/50‑1 (MQ=255)       cGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaaaa                                       <  1:2595063/50‑1 (MQ=255)       cGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaaaa                                       <  1:971172/50‑1 (MQ=255)        ggTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAg                                      <  1:2203938/50‑1 (MQ=255)        ggTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAg                                      <  1:3021632/50‑1 (MQ=255)        ggTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAg                                      >  1:2694836/1‑50 (MQ=255)        ggTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAg                                      >  1:2535964/1‑50 (MQ=255)         gTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGc                                     >  1:1752944/1‑50 (MQ=255)         gTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGc                                     <  1:4018421/50‑1 (MQ=255)           aGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGt                                   >  1:1641484/1‑50 (MQ=255)           aGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGt                                   >  1:6777204/1‑50 (MQ=255)             cAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTg                                  >  1:5606262/1‑49 (MQ=255)             cAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTg                                  >  1:5136369/1‑49 (MQ=255)              aaCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:8179269/1‑49 (MQ=255)              aaCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:5167563/1‑49 (MQ=255)              aaCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:7047285/1‑49 (MQ=255)              aaCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:5743182/1‑49 (MQ=255)              aaCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:2102045/1‑49 (MQ=255)              aaCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:6427056/1‑49 (MQ=255)              aaCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:1744385/1‑49 (MQ=255)              aaCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGa                                <  1:6393538/50‑1 (MQ=255)               aCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:8253738/1‑48 (MQ=255)               aCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGaa                               <  1:792977/50‑1 (MQ=255)                ccAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAg                              >  1:1962320/1‑50 (MQ=255)                ccAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAg                              <  1:411265/50‑1 (MQ=255)                ccAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAg                              >  1:7973608/1‑50 (MQ=255)                 cAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             <  1:2278800/50‑1 (MQ=255)                 cAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             >  1:5254049/1‑50 (MQ=255)                 cAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             <  1:4633575/50‑1 (MQ=255)                  aGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             >  1:5311446/1‑49 (MQ=255)                  aGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             >  1:1054927/1‑49 (MQ=255)                  aGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             >  1:2798576/1‑49 (MQ=255)                  aGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             >  1:4341660/1‑49 (MQ=255)                  aGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTg                            <  1:5443954/50‑1 (MQ=255)                   ggTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTg                            >  1:5832202/1‑49 (MQ=255)                   ggTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTg                            >  1:853131/1‑49 (MQ=255)                    gTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGaa                          <  1:2794309/50‑1 (MQ=255)                     tCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAg                         <  1:6758769/50‑1 (MQ=255)                      cTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAgg                        >  1:3108168/1‑50 (MQ=255)                      cTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAgg                        >  1:5193741/1‑50 (MQ=255)                         tGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAgg                        <  1:5673790/47‑1 (MQ=255)                         tGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAgg                        <  1:3114813/47‑1 (MQ=255)                         tGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTg                      <  1:4160727/49‑1 (MQ=255)                          gACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGc                     <  1:4616777/49‑1 (MQ=255)                          gACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCt                    >  1:5168800/1‑50 (MQ=255)                          gACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCt                    >  1:1668331/1‑50 (MQ=255)                           aCGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCt                    <  1:6813464/49‑1 (MQ=255)                           aCGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTg                   >  1:2704239/1‑50 (MQ=255)                           aCGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTg                   >  1:7272744/1‑50 (MQ=255)                           aCGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTg                   >  1:5438967/1‑50 (MQ=255)                           aCGCCGAAATTACCAGCGCCGGC‑AAAAAAGCGTGGAAGTGAAGGTGCTg                   <  1:989016/49‑1 (MQ=38)                            cGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTg                   >  1:8054136/1‑49 (MQ=255)                             gCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTgg                  >  1:2816287/1‑49 (MQ=255)                             gCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTgg                  >  1:8301606/1‑49 (MQ=255)                             gCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTgg                  >  1:1844526/1‑49 (MQ=255)                             gCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGa                 <  1:5650203/50‑1 (MQ=255)                             gCCGAAATTACCAGCGACGGCAAAAAAAGCGTGGAAGTGAAGGTGCTgg                  >  1:2527477/1‑49 (MQ=38)                              ccGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTgg                  >  1:7740385/1‑48 (MQ=255)                              ccGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTgg                  >  1:1553325/1‑48 (MQ=255)                              ccGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGaa                <  1:3670325/50‑1 (MQ=255)                               cGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAg               >  1:8002306/1‑50 (MQ=255)                               cGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAg               <  1:1248233/50‑1 (MQ=255)                                gAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAgg              >  1:3192985/1‑50 (MQ=255)                                 aaaTTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:3192159/1‑50 (MQ=255)                                 aaaTTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:2528654/1‑50 (MQ=255)                                   aTTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCa           <  1:7428503/50‑1 (MQ=255)                                    ttACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAg          <  1:2074582/50‑1 (MQ=255)                                     tACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:3296350/1‑46 (MQ=255)                                      aCCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:3212264/1‑45 (MQ=255)                                      aCCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGa         <  1:2180357/49‑1 (MQ=255)                                       ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:3919023/1‑44 (MQ=255)                                       ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGAt        <  1:4537410/49‑1 (MQ=255)                                        cAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcg      <  1:5818836/50‑1 (MQ=255)                                         aGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcga     >  1:480273/1‑50 (MQ=255)                                           cgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    >  1:7760273/1‑49 (MQ=255)                                           cgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    >  1:5247488/1‑49 (MQ=255)                                            gcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgacga  <  1:4777950/50‑1 (MQ=255)                                               |                                               GTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCAGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATCGACGA  >  NC_000913/3091259‑3091351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑