Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,091,169	G→T	L12L (CTG→CTT)	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	3,091,169	0	G	T	100.0%	119.0 / NA	36	L12L (CTG→CTT)	rsmE	16S rRNA m(3)U1498 methyltransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (23/13);  total (23/13)

GCGGGATTCTTTTTGTTAACCCCTACCCCACGCGTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTGACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGC  >  NC_000913/3091064‑3091301                                                                                                          |                                                                                                                                     gCGGGATTCTTTTTGTTAACCCCTACCCCACGCGTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATg                                                                                                    >  2:652279/1‑140 (MQ=255)   gggATTCTTTTTGTTAAGCCCTACCCCACGCGTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATgcc                                                                                                  <  2:487229/140‑1 (MQ=255)   gggATTCTTTTTGTTAACCCCTGCCCCACGCGTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATgcc                                                                                                  <  1:422578/140‑1 (MQ=255)       ttCTTTTTGTTAACCCCTACCCCACGCGTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCa                                                                                              >  1:313371/1‑140 (MQ=255)              tGTTAACCCCTACCCCACGCGTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCatat                                                                                       <  1:168997/140‑1 (MQ=255)              tGTTAACCCCTACCCCACGCGTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCatat                                                                                       <  2:385387/140‑1 (MQ=255)                    ccccTACCCCACGCGTACAACCGCGTGGGGAGACGACGCGGATTTTCAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGgcg                                                                                 >  2:638563/1‑140 (MQ=255)                               cgcgTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCa                                                                      >  2:550143/1‑140 (MQ=255)                               cgcgTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCa                                                                      >  2:545997/1‑140 (MQ=255)                               cgcgTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCa                                                                      >  2:323093/1‑140 (MQ=255)                                gcgTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCAt                                                                     <  2:617465/140‑1 (MQ=255)                                          gcgTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCgggg                                                           >  1:150041/1‑140 (MQ=255)                                           cgTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCa                                                                      <  1:504257/128‑1 (MQ=255)                                           cgTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCa                                                                      >  2:504257/1‑128 (MQ=255)                                            gTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCa                                                         >  1:703577/1‑140 (MQ=255)                                               gggAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGc                                                      >  1:676025/1‑140 (MQ=255)                                                  agaCGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGtt                                                   >  1:699302/1‑140 (MQ=255)                                                      gacgCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCaa                                               >  2:234315/1‑140 (MQ=255)                                                       acgCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAAt                                              <  2:406279/140‑1 (MQ=255)                                                        cgcgGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGtt                                                   <  2:74610/134‑1 (MQ=255)                                                        cgcgGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGtt                                                   >  1:74610/1‑134 (MQ=255)                                                          cgGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGt                                           >  1:291234/1‑140 (MQ=255)                                                              tttttAACTATGCGTATCCCCCGCATTTATCAGCCTGAACCACTTGCCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGa                                       <  2:649683/140‑1 (MQ=255)                                                                   aaCTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTa                                  <  1:550143/140‑1 (MQ=255)                                                                   aaCTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTa                                  <  1:233579/140‑1 (MQ=255)                                                                    aCTATGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAg                                 <  1:652279/140‑1 (MQ=255)                                                                       aTGCGTATCCCCCGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCaa                              >  2:298911/1‑140 (MQ=255)                                                                                ccccGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCAACCAGGTCtt                     >  1:360727/1‑140 (MQ=255)                                                                                  ccGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCAACCAGGTCTTTg                   >  2:387021/1‑140 (MQ=255)                                                                                   cGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCAACCAGGTCTTTGa                  >  1:572611/1‑140 (MQ=255)                                                                                   cGCATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGAGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCAACCAGGTCTTTgc                  >  1:375677/1‑139 (MQ=255)                                                                                     cATTTATCATCCTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCAACCAGGTCTTTGatg                <  2:699302/140‑3 (MQ=255)                                                                                               ccTGAACCACATACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTAc      >  1:212617/1‑140 (MQ=255)                                                                                                cTGAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTAcc     >  1:377065/1‑140 (MQ=255)                                                                                                  gAACCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAg   >  1:577775/1‑140 (MQ=255)                                                                                                   aaCCACTTACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAgc  >  2:540497/1‑140 (MQ=255)                                                                                                          |                                                                                                                                     GCGGGATTCTTTTTGTTAACCCCTACCCCACGCGTACAACCGCGTGGGGAGACGACGCGGATTTTTAACTATGCGTATCCCCCGCATTTATCATCCTGAACCACTGACCAGCCATTCTCACATCGCGCTTTGCGAAGATGCCGCCAACCATATCGGGCGCGTACTGCGCATGGGGCCGGGGCAGGCGTTGCAATTGTTTGACGGTAGCAACCAGGTCTTTGACGCCGAAATTACCAGC  >  NC_000913/3091064‑3091301

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑