Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,193,350	G→A	L142L (CTG→TTG)	mnmA ←	tRNA‑specific 2‑thiouridylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,193,350	0	G	A	96.5%	90.7 / NA	29	L142L (CTG→TTG)	mnmA	tRNA‑specific 2‑thiouridylase
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (12/16);  total (12/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCGGGAGATAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGACCGGCTTTATATTCGGCAAGGAACAGTTCGAAGACGTTGTCCCAGTACTCGGCAGCAAAGTTAACGGTGTGCAGTTCAATGCCGAGCTT  >  NC_000913/1193127‑1193584                                                                                                                                                                                                                                |                                                                                                                                                                                                                                           gcCGGGAGATAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGc                                                                                                                                                                                                                 <  1:430102/251‑1 (MQ=255)      gagaTAACGGACCAGGAAATCGCGGAATTTACGTTCGCCCATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGAGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGac                                                                                                                                                                                                            >  2:175856/1‑251 (MQ=255)         aTAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGacgt                                                                                                                                                                                                          >  1:223326/1‑250 (MQ=255)           aaCGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGacgtac                                                                                                                                                                                                        <  2:90438/250‑1 (MQ=255)                cccAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATg                                                                                                                                                                                                  >  1:127885/1‑251 (MQ=255)                     gAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCgg                                                                                                                                                                                             <  2:101249/251‑1 (MQ=255)                          cgcgGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTATGCACCTGCGGTTTGACCAGTTCGTCTACCGGGAACAGGCTTTTCGCAATCGGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTTCTGTACAGACCTCGCAACAGGCGGCTGTTGCCATCGACATCGGCCCGTCTTGCGTAATGACCGGTAg                                                                                                                                                                                          <  2:45296/249‑1 (MQ=255)                          cgcgGAATTTACGTTCGCAAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGc                                                                                                                                                                                         <  1:20297/250‑1 (MQ=255)                             ggAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGata                                                                                                                                                                                     <  1:457304/251‑1 (MQ=255)                                 tttACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCCTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAAt                                                                                                                                                                                 >  1:86669/1‑251 (MQ=255)                                                         gCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCa                                                                                                                                                          <  2:54616/250‑1 (MQ=255)                                                                                  gttgtcagaccaAGATCTTCAGCAATCTTACGCCCCTGCGGTTTTTCCATTTCGCCGGCCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTAGTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGTTTTAACTTTGAt                                                                                                                                <  2:36679/246‑1 (MQ=255)                                                                                    gaccagaccaAGATCTTCAGCAATCTTACGCCCCTGCGGTTTGTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGAtct                                                                                                                              <  2:255456/251‑1 (MQ=255)                                                                                        agaccaAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCttt                                                                                                                          >  1:404652/1‑251 (MQ=255)                                                                                             aaGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGACCAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCCCCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGc                                                                                                                     >  1:32065/1‑251 (MQ=255)                                                                                                    tCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGaa                                                                                                               <  2:163912/250‑1 (MQ=255)                                                                                                         aaTCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCCTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCg                                                                                                         <  2:86669/251‑1 (MQ=255)                                                                                                                         ggTTTTTCCAGTTCGCCACCCGGGAACAGGATTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCAATCGACATCGGCCCGCCGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGAcc                                                                                         >  2:192678/1‑251 (MQ=255)                                                                                                                                         cGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGACCGGCTTTATATTCGGCa                                                                         <  1:192678/251‑1 (MQ=255)                                                                                                                                             cgtgAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGACCGGCTTTATATTCGGCAAGGa                                                                     <  1:262538/248‑1 (MQ=255)                                                                                                                                               ggAACAGGCATTGCGCAATTTGCTCATGGCTGGTCATATAAAGGAAGTAGCGCGGGTCTTTATTGCTGTCCAGACCACGCAGCCGGCGGCTCTTGCCATCGGCAGCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACATAAATCTTCTGCGGCAAATTCGAGGAATGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTTCGACCGGCTTTATATTCGGCGAGGa                                                                     <  2:104146/249‑1 (MQ=255)                                                                                                                                                    aGGNTTTGCGCAATCTGCTCAGGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGCCCGTCTTTATATTCGGCAAGGAACAGTTc                                                              <  2:410849/251‑1 (MQ=255)                                                                                                                                                                            cTGAGCGTATAAAGGACGTAGCTATGGTCTTTATTGCTGTCCAGACCCCGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGGACGTAATGACCGGAAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAACATCCGGATTCGGCGTGCGACCGGCTTTATATTCGGCAAGGAACAGCTCGAAGACGTTGTTCCAGTACTAGgc                                      >  2:333905/1‑251 (MQ=255)                                                                                                                                                                              gAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGACCGGCTTTATATTCGGCAAGGAACAGTTCGAAGACGTTGTCCCAGTACTCGgcag                                    <  2:127885/251‑1 (MQ=255)                                                                                                                                                                                               aGCTCTGGACTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGGACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCACATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGACCGGCTTTATATTCGGCACGGAACAGTTCGCAGACGTTGTCCAAGTACTTGGCCGCAAAGTTAACGGTGTGc                   >  2:320249/1‑251 (MQ=255)                                                                                                                                                                                                   ctGGTCTTTATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGACCGGCTTTATATTCGGCAAGGAACAGTTCGAAGACGTTGTCCCAGTACTCGGCAGCAAAGTTAACGGTGTGCAGtt               >  2:87385/1‑251 (MQ=255)                                                                                                                                                                                                         tttATTGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGACCGGCTTTATATTCGGCAAGGAACAGTTCGAAGACGTTGTCCCAGTACTCGGCAGCAAAGTTAACGGTGTGCAGTTCAATGc         >  2:356751/1‑251 (MQ=255)                                                                                                                                                                                                              tGCTGTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGACCGGCTTTATATTCGGCAAGGAACAGTTCGAAGACGTTGTCCCAGTACTCGGCAGCAAAGTTAACGGTGTGCAGTTCAATGCCGAGc    >  1:407900/1‑251 (MQ=255)                                                                                                                                                                                                                  gTCCAGACCACGCAACAGGCGGCTCTTGCCATCGACATCGGCCAGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATGTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGACCGGCTTTATATTCGGCAAGGAACAGTTCGAAGACGTTGTCCCAGTACTCGGCAGCAAAGTTAACGGTGTGCAGTTCAATGCCGAGCtt  <  1:436036/249‑1 (MQ=255)                                                                                                                                                                                                                                |                                                                                                                                                                                                                                           GCCGGGAGATAACGGCCCAGGAACTCGCGGAATTTACGTTCGCCAATGAAGCAAATGCCGGTAGAGTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGCCCGACGTACGTAATGACCGGTAGCGATATAATCGGCACCTAAATCTTCGGCGGCAAATTCGAGGAAGGCTTTAAATTTGATCTCTTTGTTGCACAGAATATCCGGATTCGGCGTGCGACCGGCTTTATATTCGGCAAGGAACAGTTCGAAGACGTTGTCCCAGTACTCGGCAGCAAAGTTAACGGTGTGCAGTTCAATGCCGAGCTT  >  NC_000913/1193127‑1193584

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑