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%	336.9 / NA	83	S58G (AGC→GGC)	rsmE	16S rRNA m(3)U1498 methyltransferase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (50/33);  total (50/33)

GTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCAGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATCGACGA  >  NC_000913/3091259‑3091351                                               |                                               gTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGc                                              >  1:128459/1‑49 (MQ=255) gTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGc                                              <  1:5778437/49‑1 (MQ=255) gTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGc                                              >  1:4424713/1‑49 (MQ=255)  tttGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCa                                             <  1:741649/49‑1 (MQ=255)  tttGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCa                                             >  1:6100142/1‑49 (MQ=255)   ttGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaa                                            >  1:5510692/1‑49 (MQ=255)   ttGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaa                                            >  1:6696323/1‑49 (MQ=255)     gACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaa                                          <  1:4525181/49‑1 (MQ=255)      aCGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaaa                                        <  1:1715015/50‑1 (MQ=255)      aCGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaaa                                        <  1:5767057/50‑1 (MQ=255)      aCGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaa                                         <  1:4763242/49‑1 (MQ=255)       cGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaaaa                                       <  1:3379263/50‑1 (MQ=255)        ggTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAg                                      >  1:2687432/1‑50 (MQ=255)        ggTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAg                                      >  1:3653993/1‑50 (MQ=255)        ggTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAg                                      >  1:3051145/1‑50 (MQ=255)         gTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGc                                     >  1:3944097/1‑50 (MQ=255)          tAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCg                                    >  1:1514680/1‑50 (MQ=255)          tAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCg                                    >  1:2756786/1‑50 (MQ=255)          tAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCg                                    <  1:2336038/50‑1 (MQ=255)            gCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTg                                  >  1:1877880/1‑50 (MQ=255)             cAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 <  1:5931213/50‑1 (MQ=255)             cAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTg                                  >  1:2272459/1‑49 (MQ=255)             cAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTg                                  >  1:5911354/1‑49 (MQ=255)             cAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTg                                  >  1:6370615/1‑49 (MQ=255)              aaCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:471437/1‑49 (MQ=255)              aaCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGa                                <  1:4735398/50‑1 (MQ=255)               aCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:5858014/1‑48 (MQ=255)               aCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:2725835/1‑48 (MQ=255)                ccAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAg                              >  1:305148/1‑50 (MQ=255)                 cAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             >  1:287873/1‑50 (MQ=255)                 cAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             >  1:5395955/1‑50 (MQ=255)                 cAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             <  1:2372617/50‑1 (MQ=255)                 cAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             >  1:5808585/1‑50 (MQ=255)                  aGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             >  1:1789718/1‑49 (MQ=255)                  aGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             >  1:5934957/1‑49 (MQ=255)                  aGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTg                            <  1:3602894/50‑1 (MQ=255)                   ggTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGa                           <  1:4753570/50‑1 (MQ=255)                    gTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTg                            >  1:3123271/1‑48 (MQ=255)                    gTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTg                            >  1:1401303/1‑48 (MQ=255)                    gTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTg                            >  1:2779706/1‑48 (MQ=255)                    gTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGaa                          <  1:2858231/50‑1 (MQ=255)                     tCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAg                         <  1:1918566/50‑1 (MQ=255)                      cTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAgg                        >  1:5511078/1‑50 (MQ=255)                      cTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAgg                        >  1:3606207/1‑50 (MQ=255)                         tGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAgg                        <  1:1007429/47‑1 (MQ=255)                         tGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTg                      <  1:3880491/49‑1 (MQ=255)                         tGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTg                      <  1:4961823/49‑1 (MQ=255)                          gACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGc                     <  1:5612155/49‑1 (MQ=255)                          gACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGc                     <  1:968351/49‑1 (MQ=255)                          gACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCt                    >  1:4020616/1‑50 (MQ=255)                          gACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCt                    >  1:5578229/1‑50 (MQ=255)                           aCGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTg                   >  1:3728786/1‑50 (MQ=255)                           aCGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTg                   <  1:4702495/50‑1 (MQ=255)                             gCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTgg                  >  1:984141/1‑49 (MQ=255)                             gCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTgg                  >  1:1240738/1‑49 (MQ=255)                             gCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGa                 <  1:5194375/50‑1 (MQ=255)                              ccGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTgg                  >  1:4020352/1‑48 (MQ=255)                                gAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAgg              >  1:4955932/1‑50 (MQ=255)                                gAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAgg              >  1:1321375/1‑50 (MQ=255)                                gAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAgg              >  1:6513168/1‑50 (MQ=255)                                 aaaTTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             <  1:3677539/50‑1 (MQ=255)                                  aaTTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:5206994/1‑49 (MQ=255)                                   aTTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGATGGAAGGCCa           <  1:4211535/50‑1 (MQ=38)                                      aCCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:5265266/1‑45 (MQ=255)                                      aCCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:6595836/1‑45 (MQ=255)                                      aCCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:2733285/1‑45 (MQ=255)                                       ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGAt        <  1:4614421/49‑1 (MQ=255)                                       ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGAt        <  1:6178898/49‑1 (MQ=255)                                       ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGAt        <  1:3538408/49‑1 (MQ=255)                                       ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATc       <  1:1999301/50‑1 (MQ=255)                                        cAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcg      <  1:2227290/50‑1 (MQ=255)                                        cAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATc       >  1:208595/1‑49 (MQ=255)                                         aGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcga     >  1:1916796/1‑50 (MQ=255)                                         aGCGCCGGCAAAAAAAGCGTGGAAGCGAAGGTGCTGGAAGGCCAGATcga     >  1:3510080/1‑50 (MQ=38)                                          gcgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    <  1:2954066/50‑1 (MQ=255)                                          gcgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    >  1:2703824/1‑50 (MQ=255)                                          gcgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    <  1:2083309/50‑1 (MQ=255)                                          gcgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    >  1:3088586/1‑50 (MQ=255)                                           cgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgacg   <  1:5611227/50‑1 (MQ=255)                                           cgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    >  1:898576/1‑49 (MQ=255)                                            gcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgacga  <  1:542182/50‑1 (MQ=255)                                            gcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgacga  >  1:12253/1‑50 (MQ=255)                                            gcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgacga  >  1:1131248/1‑50 (MQ=255)                                               |                                               GTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCAGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATCGACGA  >  NC_000913/3091259‑3091351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑