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%	153.6 / NA	49	*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 (24/25);  total (24/25)

CTGCCCGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAGTTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCG  >  NC_000913/3781554‑3781816                                                                                                                                       |                                                                                                                                 ctgcccGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTAc                                                                                                                              >  2:514892/1‑139 (MQ=255) ctgcccGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTAc                                                                                                                              >  2:139242/1‑139 (MQ=255)   gcccGTTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTg                                                                                                                            >  2:319226/1‑139 (MQ=255)         tGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGcc                                                                                                                      <  1:636847/139‑1 (MQ=255)              aaaaaaTTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATa                                                                                                                 <  1:139242/139‑1 (MQ=255)              aaaaaaTTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATa                                                                                                                 <  1:319226/139‑1 (MQ=255)                                   tGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGc                                                                                            <  2:7525/139‑1 (MQ=255)                                      cGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACg                                                                                         <  1:514892/139‑1 (MQ=255)                                        gACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGAt                                                                                       <  1:166025/139‑1 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATa                                                                                                                 <  1:1119181/108‑1 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATa                                                                                                                 >  2:1119181/1‑108 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAg                                                                                  >  2:571271/1‑139 (MQ=255)                                             ccGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAg                                                                                  >  1:510771/1‑139 (MQ=255)                                                             tCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCa                                                                                                  >  2:704369/1‑107 (MQ=255)                                                             tCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCa                                                                                                  <  1:704369/107‑1 (MQ=255)                                                             tCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGatcc                                                                      >  2:542209/1‑135 (MQ=255)                                                             tCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGatcc                                                                      <  1:542209/135‑1 (MQ=255)                                                                                 ggtgTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGt                                              >  2:88596/1‑139 (MQ=255)                                                                                    gtATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTaa                                           <  1:571271/139‑1 (MQ=255)                                                                                     tATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAAt                                          >  1:1100342/1‑139 (MQ=255)                                                                                             cTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCGGGCACGATCACAGGACATTAGATACCATCCCCATACTCAAATGTATGGTTAATACCGTTGa                                  >  2:724609/1‑139 (MQ=255)                                                                                               ggggacAGTTGAGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTAt                                                 >  2:659360/6‑122 (MQ=255)                                                                                               ggcggcAGTTGGTGTATCCGGGAGCGGTATTGAGAGAATAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCa                                                                                           <  2:795038/80‑1 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCgg                                                                                             >  1:547599/1‑78 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCgg                                                                                             <  2:547599/78‑1 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCa                                                                                           >  1:795038/1‑80 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                   <  2:243991/120‑1 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                   >  1:243991/1‑120 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTAt                                                 <  1:659360/122‑1 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGaaa                                <  2:1100342/139‑1 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGCCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGaaa                                >  2:717146/1‑139 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGG‑TAGATGATTACAt                                                                                                      <  2:1069744/68‑1 (MQ=255)                                                                                               ggcggcAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGG‑TAGATGATTACAt                                                                                                      >  1:1069744/1‑68 (MQ=255)                                                                                                       ttGGGGTATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTc                        <  1:88596/139‑1 (MQ=255)                                                                                                             tATCCGGGAGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATc                  <  2:510771/139‑1 (MQ=255)                                                                                                                     aGCGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATg          >  1:946827/1‑139 (MQ=255)                                                                                                                       cGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                   >  2:934376/1‑96 (MQ=255)                                                                                                                       cGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                   <  1:934376/96‑1 (MQ=255)                                                                                                                       cGGTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGc        >  2:391077/1‑139 (MQ=255)                                                                                                                         gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCAc                                                                                          <  1:754597/55‑1 (MQ=255)                                                                                                                         gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCAc                                                                                          >  2:754597/1‑55 (MQ=255)                                                                                                                         gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                   <  2:312524/94‑1 (MQ=255)                                                                                                                         gTATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGt                                                   >  1:312524/1‑94 (MQ=255)                                                                                                                          tATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTa     <  1:391077/139‑1 (MQ=255)                                                                                                                          tATTGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTa     >  2:818646/1‑139 (MQ=255)                                                                                                                             tGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCg  <  2:1011316/139‑1 (MQ=255)                                                                                                                             tGAGAGATTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCg  <  1:1016095/139‑1 (MQ=255)                                                                                                                                 agaTTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATcccc                                                               <  2:110104/74‑1 (MQ=255)                                                                                                                                 agaTTAATTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATcccc                                                               >  1:110104/1‑74 (MQ=255)                                                                                                                                       |                                                                                                                                 CTGCCCGCTGAACAAAAAATTCGCATTCCGATGGTGCCGGACAGCCGCAGCATGAATCTGTCCAATGCGGTGTCGGTAGTGGTGTATGAAGCCTGGCGGCAGTTGGGGTATCCGGGAGCGGTATTGAGAGATTAGTTACTGTAGGCCGGATAGATGATTACATCGCATCCGGCACGATCACAGGACATTAGATCCCATCCCCATACTCAAATGTATGGTTAATACCGTTGAAATGCTGGTCCATATCCATTGATGGCTTATCG  >  NC_000913/3781554‑3781816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑