Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,781,688	G→A	*158* (TAG→TAA)	trmL →	tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,781,688	0	G	A	100.0%	171.8 / NA	53	*158* (TAG→TAA)	trmL	tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (22/31);  total (22/31)

CCTGCCCGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAGTTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCGCTGTCT  >  NC_000913/3781553‑3781822                                                                                                                                         |                                                                                                                                       cctgcccGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGattaatta                                                                                                                                     >  2:165183/1‑139 (MQ=255)  ctgcccGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGGATCCGGGGGCGGTATTTAGAGATTAATTAc                                                                                                                                    >  2:998006/1‑139 (MQ=255)    gcccGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTg                                                                                                                                  >  1:1292979/1‑139 (MQ=255)        gCTGAACACAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAgg                                                                                                                              <  1:846554/139‑1 (MQ=255)        gCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAgg                                                                                                                              <  1:1165517/139‑1 (MQ=255)           gAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCg                                                                                                                           <  2:205202/139‑1 (MQ=255)             aCAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGa                                                                                                                         <  2:410118/139‑1 (MQ=255)                            tCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCC‑GGAGCGGTATTGAGAGATTAATTACTGTAGGc                                                                                                                             <  2:679002/119‑1 (MQ=255)                            tCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCC‑GGAGCGGTATTGAGAGATTAATTACTGTAGGc                                                                                                                             >  1:679002/1‑119 (MQ=255)                                 tGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATcc                                                                                                     <  1:1009055/139‑1 (MQ=255)                                      ccGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCa                                                                                                 <  1:1295660/138‑1 (MQ=255)                                      ccGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCa                                                                                                 >  2:1295660/1‑138 (MQ=255)                                      ccGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCAc                                                                                                >  2:389686/1‑139 (MQ=255)                                           cAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACGTCGCATCCGGCACGATca                                                                                           <  1:760002/139‑1 (MQ=255)                                           cAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATca                                                                                           <  2:477606/139‑1 (MQ=255)                                             gCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                         <  1:165183/139‑1 (MQ=255)                                              ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGAt                                                                                             <  1:1345412/135‑1 (MQ=255)                                              ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGAt                                                                                             >  2:1345412/1‑135 (MQ=255)                                               cGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATca                                                                                           >  2:1264137/1‑135 (MQ=255)                                               cGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATca                                                                                           <  1:1264137/135‑1 (MQ=255)                                                              tCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGatcccatc                                                                        >  2:719914/1‑139 (MQ=255)                                                              tCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGatcccatc                                                                        >  1:867904/1‑139 (MQ=255)                                                                      ggTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACt                                                                <  1:656030/139‑1 (MQ=255)                                                                        tgtCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCa                                                              >  1:413904/1‑139 (MQ=255)                                                                        tgtCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCa                                                              >  2:748763/1‑139 (MQ=255)                                                                             gTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                         <  2:413904/139‑1 (MQ=255)                                                                             gTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                         <  2:358546/139‑1 (MQ=255)                                                                             gTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTAAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                         <  2:867904/139‑1 (MQ=255)                                                                               aGTGGTGTATGACGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGCACATTAGATCCCATCCCCATACTCAAATGTAt                                                       <  1:813934/139‑1 (MQ=255)                                                                                 tggtgTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCAc                                                                                                <  1:756564/96‑1 (MQ=255)                                                                                 tggtgTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCAc                                                                                                >  2:756564/1‑96 (MQ=255)                                                                                      tATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATcccc                                                                     >  2:417765/1‑118 (MQ=255)                                                                                      tATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATcccc                                                                     <  1:417765/118‑1 (MQ=255)                                                                                       aTGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATa                                               <  1:389686/139‑1 (MQ=255)                                                                                           aGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGt                                           >  1:983898/1‑139 (MQ=255)                                                                                             ccTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATca                                                                                           >  2:37061/1‑89 (MQ=255)                                                                                             ccTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATca                                                                                           <  1:37061/89‑1 (MQ=255)                                                                                                ggcggcAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCg                                                                                                          >  1:1159711/1‑71 (MQ=255)                                                                                                ggcggcAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCg                                                                                                          <  2:1159711/71‑1 (MQ=255)                                                                                                ggcggcAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGAt                                                                                             >  2:953546/1‑84 (MQ=255)                                                                                                ggcggcAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGAt                                                                                             <  1:953546/84‑1 (MQ=255)                                                                                                  cggcAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAGATGTATGGTTAATACCGTTGAAATg                                    <  1:719914/139‑1 (MQ=255)                                                                                                  cggcAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATg                                    <  2:1292979/139‑1 (MQ=255)                                                                                                    gcAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCt                                  <  1:748763/139‑1 (MQ=255)                                                                                                      aGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                         <  2:157867/82‑1 (MQ=255)                                                                                                      aGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                         >  1:157867/1‑82 (MQ=255)                                                                                                                 tCCGGGAGCGGTATTGAGAGATTAATTACTGTAgg                                                                                                                              <  2:183879/35‑1 (MQ=255)                                                                                                                 tCCGGGAGCGGTATTGAGAGATTAATTACTGTAgg                                                                                                                              >  1:183879/1‑35 (MQ=37)                                                                                                                         cGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGc              >  1:1321659/1‑139 (MQ=255)                                                                                                                           gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCtt            >  2:590967/1‑139 (MQ=255)                                                                                                                            tATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                         <  2:1064121/93‑1 (MQ=255)                                                                                                                            tATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                         >  1:1064121/1‑93 (MQ=255)                                                                                                                               tGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCg        <  1:343724/139‑1 (MQ=255)                                                                                                                                    gaTTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCa                                                                    >  2:663710/1‑74 (MQ=255)                                                                                                                                    gaTTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCa                                                                    <  1:663710/74‑1 (MQ=255)                                                                                                                                     attaattaCTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCg        >  2:1013207/1‑133 (MQ=255)                                                                                                                                     attaattaCTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCg        <  1:1013207/133‑1 (MQ=255)                                                                                                                                     attaattaCTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCGCTGTCt  >  1:255499/1‑139 (MQ=255)                                                                                                                                     attaattaCTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCGCTGTCt  >  2:713898/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                       CCTGCCCGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTT‑GGGGTATCCGGGAGCGGTATTGAGAGATTAGTTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCGCTGTCT  >  NC_000913/3781553‑3781822

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑