Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,163,286	(A)5→4	intergenic (‑16/‑353)	trmA ← / → btuB	tRNA m(5)U54 methyltransferase/cobalamin/cobinamide outer membrane transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,163,282	0	A	.	100.0%	138.9 / NA	33	intergenic (‑12/‑357)	trmA/btuB	tRNA m(5)U54 methyltransferase/cobalamin/cobinamide outer membrane transporter
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (17/16);  total (17/16)

TGCAAACGTACCACTTTTTCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTGAAAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTCCAGATCTTGATGAATTCCTATTTGTGAGCTA  >  NC_000913/4163203‑4163358                                                                                |                                                                             tGCAAACGTACCACTTTTTCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTGa                                                                              <  2:778420/80‑1 (MQ=255)        gTACCACTTTTTCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTGaaaatta                                                                        >  2:778463/1‑76 (MQ=255)         tACCACTTTTTCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAg                                                                    <  1:778424/81‑1 (MQ=255)              cTTTTTCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTAcgc                                                               >  2:778476/1‑81 (MQ=255)                ttttCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACgcgg                                                             >  1:778463/1‑81 (MQ=255)                 tttCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTAcgcg                                                              <  1:778426/79‑1 (MQ=255)                 tttCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACgcggc                                                            >  1:778471/1‑81 (MQ=255)                 tttCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACgcggc                                                            >  1:778461/1‑81 (MQ=255)                 tttCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACgcgg                                                             <  1:778425/80‑1 (MQ=255)                  ttCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACgcggc                                                            >  1:778468/1‑80 (MQ=255)                   tCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGa                                                          >  1:778479/1‑81 (MQ=255)                     ggCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGAt                                                         <  2:778426/80‑1 (MQ=255)                       cTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGt                                                      <  2:778427/81‑1 (MQ=255)                        tAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTg                                                       >  1:778475/1‑79 (MQ=255)                         aaCTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAg                                                    >  1:778469/1‑81 (MQ=255)                          aCTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAgg                                                   <  1:778429/81‑1 (MQ=255)                          aCTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAg                                                    <  2:778429/80‑1 (MQ=255)                           cTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAggg                                                  <  2:778430/81‑1 (MQ=255)                            tGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGa                                                 >  2:778484/1‑81 (MQ=255)                              cgcTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGAtt                                               <  1:778432/81‑1 (MQ=255)                                     tACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCtcatc                                        <  2:778432/81‑1 (MQ=255)                                     tACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCtcat                                         >  1:778476/1‑80 (MQ=255)                                       ctgttctgttGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCtcat                                         >  2:778486/1‑78 (MQ=255)                                            ctgttGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTc                                 >  1:778478/1‑81 (MQ=255)                                             tgttGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTc                                 >  2:778489/1‑80 (MQ=255)                                               ttGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTcc                                <  1:778435/79‑1 (MQ=255)                                               ttGGAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTCCAg                              <  1:778434/81‑1 (MQ=255)                                                  gAAGGTGTTCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTCCAGATc                           <  1:778436/81‑1 (MQ=255)                                                         ttCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTCCAGATCTtgatga                    <  1:778437/81‑1 (MQ=255)                                                         ttCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTCCAGATCTtgatg                     >  1:778481/1‑80 (MQ=255)                                                          tCGGGGGTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTCCAGATCTTGATGaa                   >  2:778493/1‑81 (MQ=255)                                                              gggTCATGATGTATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTCCAGATCTTGATGAATTcc               <  1:778438/81‑1 (MQ=255)                                                                         tATCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTCCAGATCTTGATGAATTCCTATTTGTGAGc    <  1:778439/81‑1 (MQ=255)                                                                          aTCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTCCAGATCTTGATGAATTCCTATTTGTGAGc    >  2:778479/1‑80 (MQ=255)                                                                           tCCTG‑AAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTCCAGATCTTGATGAATTCCTATTTGTGAGCTa  >  1:778440/1‑81 (MQ=255)                                                                                |                                                                             TGCAAACGTACCACTTTTTCGGCTAACTGCGCTTCATACTGTTCTGTTGGAAGGTGTTCGGGGGTCATGATGTATCCTGAAAAATTAAAGTACGCGGCGATTGTAGGGATTGCTCATCAGATGTCCAGATCTTGATGAATTCCTATTTGTGAGCTA  >  NC_000913/4163203‑4163358

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑