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%	212.0 / NA	67	*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 (28/39);  total (28/39)

CTGCCCGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAGTTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCGCTGTCT  >  NC_000913/3781554‑3781822                                                                                                                                       |                                                                                                                                       ctgcccGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTAc                                                                                                                                    >  1:444308/1‑139 (MQ=255) ctgcccGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTAc                                                                                                                                    >  2:454911/1‑139 (MQ=255) atgcccGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGAAAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTGGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGAATTGAGAGATTAATTAc                                                                                                                                    >  1:661553/2‑139 (MQ=255)    cccGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGt                                                                                                                                 >  1:994714/1‑139 (MQ=255)    cccGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGt                                                                                                                                 <  2:444308/139‑1 (MQ=255)       gCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAgg                                                                                                                              <  1:293092/139‑1 (MQ=255)         tGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGcc                                                                                                                            >  2:849335/1‑139 (MQ=255)           aaCAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCgg                                                                                                                          >  2:896088/1‑139 (MQ=255)            aCAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGa                                                                                                                         <  1:482061/139‑1 (MQ=255)             cAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGAt                                                                                                                        <  2:309995/139‑1 (MQ=255)              aaaaaaTTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATa                                                                                                                       <  2:397123/139‑1 (MQ=255)                     tCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGAtt                                                                                                                >  2:490408/1‑139 (MQ=255)                                   tGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGCATTGAGAGATTAATTACTGTAAGCCGGATAGATGATTACATCGCATCCGGc                                                                                                  <  2:661553/139‑1 (MQ=255)                                     ccGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCAc                                                                                                >  2:550850/1‑139 (MQ=255)                                     ccGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCAc                                                                                                <  2:965324/139‑1 (MQ=255)                                            gCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                         <  2:125280/139‑1 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTa                                                                                                                                >  1:659974/1‑99 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTa                                                                                                                                <  2:659974/99‑1 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCa                                                                                                        <  1:541229/123‑1 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCa                                                                                                        >  2:541229/1‑123 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAg                                                                                        <  2:885759/139‑1 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAg                                                                                        >  2:762348/1‑139 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAg                                                                                        >  1:48527/1‑139 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAg                                                                                        <  1:896088/139‑1 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATCAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCAAGATCCCAg                                                                                        <  2:222627/139‑1 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGACTGGCGGCAGGTGGGGTATCCGGGAGTGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAg                                                                                        <  2:347803/139‑1 (MQ=255)                                               gcagcaTGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGTGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATAACAggc                                                                                      <  2:672199/139‑2 (MQ=255)                                                       aaTCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGat                                                                              <  2:800947/139‑1 (MQ=255)                                                            gTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGatcccat                                                                         <  1:490408/139‑1 (MQ=255)                                                            gTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGatcccat                                                                         <  1:762348/139‑1 (MQ=255)                                                             tCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGatcccatc                                                                        >  2:491608/1‑139 (MQ=255)                                                              ccAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGatcccatcc                                                                       <  1:550850/139‑1 (MQ=255)                                                                       tgtCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCa                                                              >  1:757294/1‑139 (MQ=255)                                                                            gTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                         <  2:757294/139‑1 (MQ=255)                                                                            gTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                         <  2:994714/139‑1 (MQ=255)                                                                               gtggtgTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATg                                                      >  1:565861/1‑139 (MQ=255)                                                                                tggtgTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACt                                                                                                                                   <  1:449161/61‑1 (MQ=255)                                                                                tggtgTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACt                                                                                                                                   >  2:449161/1‑61 (MQ=255)                                                                                tggtgTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                         >  2:745186/1‑135 (MQ=255)                                                                                tggtgTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                         <  1:745186/135‑1 (MQ=255)                                                                                 ggtgTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                         <  1:342572/102‑1 (MQ=255)                                                                                 ggtgTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                         >  2:342572/1‑102 (MQ=255)                                                                                    gtATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTaa                                                 <  1:454911/139‑1 (MQ=255)                                                                                            ccTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                         >  1:1045412/1‑91 (MQ=255)                                                                                            ccTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                         <  2:1045412/91‑1 (MQ=255)                                                                                             cTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGa                                        >  1:819262/1‑139 (MQ=255)                                                                                             cTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGa                                        >  1:769296/1‑139 (MQ=255)                                                                                               ggcggcAGTTGGGGTATGCGGGAGCGGTATTGAGAGATTAATTGCTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATAc                                              >  2:501644/1‑131 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATa                                                                                                                       <  1:741970/58‑1 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATa                                                                                                                       >  2:741970/1‑58 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCa                                                              <  2:287319/115‑1 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCa                                                              >  1:287319/1‑115 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATAc                                              <  1:501644/131‑1 (MQ=255)                                                                                                  ggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTGCATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGc                                   <  2:769296/139‑1 (MQ=255)                                                                                                   gcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCATGATCACAGGACATTAGATCCCATCCCCATACTCAAATCTATGGTTAATACCGTTGAAATGCt                                  <  2:727253/139‑1 (MQ=255)                                                                                                       ttGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTc                              <  2:565861/139‑1 (MQ=255)                                                                                                            gTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCatat                         <  1:849335/139‑1 (MQ=255)                                                                                                                         gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCa                                                                                                        <  2:391503/47‑1 (MQ=255)                                                                                                                         gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCa                                                                                                        >  1:391503/1‑47 (MQ=255)                                                                                                                         gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                         >  2:207870/1‑62 (MQ=255)                                                                                                                         gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATcaca                                                                                         <  1:207870/62‑1 (MQ=255)                                                                                                                             tGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCg        <  2:819262/139‑1 (MQ=255)                                                                                                                               agagaTTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCGCt      <  1:491608/139‑1 (MQ=255)                                                                                                                                 agaTTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCt                                  >  1:931060/1‑109 (MQ=255)                                                                                                                                 agaTTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCt                                  <  2:931060/109‑1 (MQ=255)                                                                                                                                   attaattaCTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCGCTGTCt  >  1:454645/1‑139 (MQ=255)                                                                                                                                    ttAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTaa                                                 >  2:627351/1‑91 (MQ=255)                                                                                                                                    ttAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTaa                                                 <  1:627351/91‑1 (MQ=255)                                                                                                                                       |                                                                                                                                       CTGCCCGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAGTTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCGCTGTCT  >  NC_000913/3781554‑3781822

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑