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%	266.3 / NA	66	S58G (AGC→GGC)	rsmE	16S rRNA m(3)U1498 methyltransferase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (28/38);  total (28/38)

TTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCAGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATCGACGA  >  NC_000913/3091261‑3091351                                             |                                               ttGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaa                                            >  1:4319163/1‑49 (MQ=255) ttGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaa                                            >  1:4575881/1‑49 (MQ=255)  tGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaa                                           <  1:1731368/49‑1 (MQ=255)   gACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaa                                          >  1:3874726/1‑49 (MQ=255)   gACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaa                                          >  1:1522379/1‑49 (MQ=255)    aCGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaaa                                        <  1:307636/50‑1 (MQ=255)    aCGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaa                                         <  1:1309321/49‑1 (MQ=255)    aCGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaa                                         >  1:458853/1‑49 (MQ=255)     cGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaaaa                                       <  1:275841/50‑1 (MQ=255)     cGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaaaa                                       <  1:1687838/50‑1 (MQ=255)     cGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCaaaaaaa                                       <  1:5064060/50‑1 (MQ=255)      ggTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAg                                      <  1:3864363/50‑1 (MQ=255)       gTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGc                                     <  1:4789963/50‑1 (MQ=255)         aGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCTGGCAAAAAAAGCGt                                   >  1:3498695/1‑50 (MQ=255)         aGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGt                                   >  1:4484448/1‑50 (MQ=255)          gCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGt                                   <  1:1350434/49‑1 (MQ=255)          gCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTg                                  >  1:1486932/1‑50 (MQ=255)           cAACCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTg                                  >  1:769949/1‑49 (MQ=255)            aaCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTgg                                 >  1:3351047/1‑49 (MQ=255)            aaCCAGGTCTTTGACGCCGAAATAACCAGCGCCGGCAAAAAAAGCGTGGa                                <  1:457010/50‑1 (MQ=39)             aCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGaa                               <  1:446467/50‑1 (MQ=255)             aCCAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGaa                               <  1:651262/50‑1 (MQ=255)               cAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             >  1:4117826/1‑50 (MQ=255)               cAGGTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGt                             <  1:3741000/50‑1 (MQ=255)                  gTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTg                            >  1:2394432/1‑48 (MQ=255)                  gTCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGaa                          <  1:2983110/50‑1 (MQ=255)                   tCTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAg                         <  1:3564679/50‑1 (MQ=255)                    cTTTGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAgg                        >  1:1854101/1‑50 (MQ=255)                       tGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAgg                        <  1:4267844/47‑1 (MQ=255)                       tGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGt                       <  1:715903/48‑1 (MQ=255)                       tGACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGc                     >  1:803746/1‑50 (MQ=255)                        gACGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCt                    >  1:1229049/1‑50 (MQ=255)                         aCGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCt                    <  1:3401804/49‑1 (MQ=255)                         aCGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTg                   <  1:2272589/50‑1 (MQ=255)                         aCGCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTg                   >  1:1689908/1‑50 (MQ=255)                           gCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTgg                  >  1:3422330/1‑49 (MQ=255)                           gCCGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTgg                  >  1:4057487/1‑49 (MQ=255)                             cGAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAg               <  1:38427/50‑1 (MQ=255)                              gAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAgg              >  1:612713/1‑50 (MQ=255)                              gAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAgg              >  1:3399316/1‑50 (MQ=255)                              gAAATTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAgg              >  1:2187642/1‑50 (MQ=255)                               aaaTTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:4111594/1‑50 (MQ=255)                               aaaTTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             <  1:3754365/50‑1 (MQ=255)                                aaTTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGcc            <  1:3251756/50‑1 (MQ=255)                                aaTTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:2561132/1‑49 (MQ=255)                                 aTTACCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCa           <  1:39024/50‑1 (MQ=255)                                    aCCAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGa         <  1:5011824/49‑1 (MQ=255)                                     ccAGCGCCGGCAAAAAGAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGAt        <  1:4109967/49‑1 (MQ=39)                                     ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGc             >  1:2731982/1‑44 (MQ=255)                                     ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGAt        <  1:1834886/49‑1 (MQ=255)                                     ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATc       <  1:3404786/50‑1 (MQ=255)                                     ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATc       <  1:5133642/50‑1 (MQ=255)                                     ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATc       <  1:1827090/50‑1 (MQ=255)                                     ccAGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATc       <  1:2649822/50‑1 (MQ=255)                                       aGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcga     <  1:2217921/50‑1 (MQ=255)                                       aGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcga     >  1:2162314/1‑50 (MQ=255)                                       aGCGCCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcga     <  1:3909741/50‑1 (MQ=255)                                        gcgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    <  1:1409100/50‑1 (MQ=255)                                        gcgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    <  1:707897/50‑1 (MQ=255)                                        gcgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    <  1:1077264/50‑1 (MQ=255)                                        gcgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    <  1:2470637/50‑1 (MQ=255)                                         cgcCGGCAAAGAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgacg   <  1:276098/50‑1 (MQ=255)                                         cgcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgac    >  1:2976030/1‑49 (MQ=255)                                          gcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgacga  >  1:2328783/1‑50 (MQ=255)                                          gcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgacga  <  1:685817/50‑1 (MQ=255)                                          gcCGGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATcgacga  >  1:1355515/1‑50 (MQ=255)                                             |                                               TTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGCGCCAGCAAAAAAAGCGTGGAAGTGAAGGTGCTGGAAGGCCAGATCGACGA  >  NC_000913/3091261‑3091351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑