Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,880,370	G→T	18.1%	Q61H (CAG→CAT)	mnmE →	tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,880,370	0	G	T	18.1%	61.9 / 3.0	22	Q61H (CAG→CAT)	mnmE	tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase
Reads supporting (aligned to +/- strand):  ref base G (10/8);  new base T (2/2);  total (12/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.34e-01

TAAGCACCGCGCATCCGCCACACAAAGCAACAGGAACATCATGAGCGATAATGACACTATCGTAGCCCAGGCCACGCCTCCGGGACGTGGCGGCGTTGGCATCCTGCGCATCTCCGGCTTCAAAGCCCGTGAAGTTGCCGAAACCGTGCTGGGTAAACTGCCTAAGCCGCGCTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCAAGGTCATGGCGGTCCGGTGATCCTCGACCTGCTGTTAAAACGCATTCTGACCATTCCCGGCCTGCGGATTGCTCGCCCTGGTGAGTTTTCCGAACGCGCGTTTCTTAACGATAAACTTGACTTAGCCCAGGCCGAGGCGATTGCCGATCTTATCGACGCCAGTTCGGAACAGGCGGCCCGTTCGGCAC  >  CP009273/3880148‑3880620                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                           gaaccACCCCGCACCCCCCCCACAAACCAACAGGAACATCATGCGCGTTAATGCCATTATCGTTGCCCAGGCCACGCCTCCGGGACGTGGCGGCGTTGGCTTCCTGCGCATCTCCGGCTTCAAGGCCCGTGAAGTTGCCGAAACCGTGCTGGGTAAACTGCCTAAGCCGCGCTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGc                                                                                                                                                                                                        <  2:438759/271‑1 (MQ=255)          cgcATCCGCCACACAAAGCAACAGGAACATCATGAGCGATAATGACACTATCGTAGCCCAGGCCACGCCTCCGGGACGTGGCGGCGTTGGCATCCTGCGCATCTCCGGCTTCAAAGCCCGTGAAGTTGCCGAAACCGTGCTGGGTAACCTGCCTAAGCNGCGCTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGACCTCGTTCACCGGCGAAGATGTGCTGGAAcgg                                                                                                                                                                                                >  1:447035/1‑272 (MQ=255)                                                aTAATGACACTATCGTAGCCCAGTCCACTCCTCAGGGACGTGGCGGCGTTGGCATCCTGCGCATCTCCGGCTTCAAAGCCCGTGAAGTTGCCGAAACCGTGCTGGGTAAACTGCCTAAGCCGCGCTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGNGCTATGGTTCCCTGGccagca                                                                                                                                                                                                                               >  1:351017/1‑201 (MQ=255)                                                          tatcgcgccccAGGCCCCGCCGCCGCGACGGGGCGGCGTTGGCATCCTGCGCATCCACGGCTTCAAAGCCCGTGAAGGTGCCGAAACCGTGCGGGGTAAACTGCCTAAGCCGCGCTACGCCGATTATCTTACGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCAAGGTCATGGCGGTCCGGTGATCCTCGACCTGCTGTTAAAACGCAtt                                                                                                                                                <  2:447022/266‑1 (MQ=255)                                                                      ggCCACGCCTCCGGGACGTGGCGGCGTTGGCATCCTGCGCATCTCCGGCTTCAAAGCCCGTGAAGTTGCCGAAACCGTGCTGGGTAAACTGCCTAAGCCGCGCTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCATGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAAc                                                                                                                                                                                                  >  1:254918/1‑212 (MQ=255)                                                                      ggCCACGCCTCCGGGACGTGGCGGCGTTGGCATCCTGCGCATCTCCGGCTTCAAAGCCCGTGAAGTTGCCGAAACCGTGCTGGGTAAACTGCCTAAGCCGCGCTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCAAGGTCATGGCGGTCCGGTGGTCCCCCACCTGCTGTTAAAACGCCTTCTGACCATTccc                                                                                                                                    >  2:144653/1‑274 (MQ=255)                                                                      ggCCACGCCTCCGGGACGTGGCGGCGTTGGCATCCTGCGCATCTCCGGCTTCAAAGCCCGTGAAGTTGCCGAAACCGTGCTGGGTAAACTGCCTAAGCCGCGCTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCAAGGTCATGGCGGTCCGGTGATCCTc                                                                                                                                                                     >  1:172004/1‑241 (MQ=255)                                                                          aagCCTCCGGGACGTGGCGGCGTTGGCATCCTGCGCATCTCCGGCTTCAAAGCCCGTGAAGTTGCCGAAACCGTGCTGGGTAAACTGCCTAAGCCGCGCTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCATGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCa                                                                                                                                                                                              <  2:254910/210‑1 (MQ=255)                                                                          aCGCCTCCGGGACGTGGCGGCGTTGGCATCCTGCGCATCTCCGGCTTCAAAGCCCGTGAAGTTGCCGAAACCGTGCTGGGTAAACTGCCTAAGCCGCGCTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCAAGGTCATGGCGGTCCGGTGATCCTCGAcc                                                                                                                                                                 <  2:171998/241‑1 (MQ=255)                                                                                                                                                                           gcTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGaa                                                                                                                                                                                                                               >  2:264638/1‑82 (MQ=255)                                                                                                                                                                           gcTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCg                                                                                                                                                                                                                 >  2:236412/1‑96 (MQ=255)                                                                                                                                                                               cGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCg                                                                                                                                                                                                                           <  1:264646/82‑1 (MQ=255)                                                                                                                                                                               cGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGa                                                                                                                                                                                                             <  1:236419/96‑1 (MQ=255)                                                                                                                                                                                  cGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCATGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTg                                                                                                                                                                                                      >  2:424681/1‑100 (MQ=255)                                                                                                                                                                                      tATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCATGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAAc                                                                                                                                                                                                  <  1:424694/100‑1 (MQ=255)                                                                                                                                                                                                       cGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCAAGGTCATGGCGGTCCGGTGATCCTCGACCTGATGTTAAAACGCATTCTGACCATTCCCGGCCTGCGGATTTCTCGCCCTGGTGAGTTTTCCGACCGCGCGGTTCTTAACGATAAACTTGACTTACCCCAGGCCGAGGCGCTTTCCGATCTAAATGACGCCACGTCGGAACAGGCCGACCgggcgggac  >  2:493903/1‑267 (MQ=255)                                                                                                                                                                                                        gCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCAAGGTCATGGCGGTCCGGTGATCCTCGACCTGCTGTTAAAACGCATTc                                                                                                                                               >  1:451020/1‑133 (MQ=255)                                                                                                                                                                                                            aCGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGaa                                                                                                                                                                                                   >  2:338224/1‑77 (MQ=255)                                                                                                                                                                                                            aCGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCAAGGTCATGGCGGTCCGGTGATCCTCGACCTGCTGTTAAAACGCATTCTGAc                                                                                                                                           <  2:451007/133‑1 (MQ=255)                                                                                                                                                                                                                cAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGc                                                                                                                                                                                               <  1:338235/77‑1 (MQ=255)                                                                                                                                                                                                                     tGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCAAGGTCATGGCGGTCCGGTGATCCTCGACCTGCTGTTAAAACGCATTc                                                                                                                                               >  2:201750/1‑120 (MQ=255)                                                                                                                                                                                                                         cGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCAAGGTCATGGCGGTCCGGTGATCCTCGACCTGCTGTTAAAACGCATTCTGAc                                                                                                                                           <  1:201756/120‑1 (MQ=255)                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                           TAAGCACCGCGCATCCGCCACACAAAGCAACAGGAACATCATGAGCGATAATGACACTATCGTAGCCCAGGCCACGCCTCCGGGACGTGGCGGCGTTGGCATCCTGCGCATCTCCGGCTTCAAAGCCCGTGAAGTTGCCGAAACCGTGCTGGGTAAACTGCCTAAGCCGCGCTACGCCGATTATCTTCCGTTTAAAGACGCCGACGGCAGCGTGCTCGATCAGGGGATTGCGCTATGGTTCCCTGGCCCGAACTCGTTCACCGGCGAAGATGTGCTGGAACTGCAAGGTCATGGCGGTCCGGTGATCCTCGACCTGCTGTTAAAACGCATTCTGACCATTCCCGGCCTGCGGATTGCTCGCCCTGGTGAGTTTTCCGAACGCGCGTTTCTTAACGATAAACTTGACTTAGCCCAGGCCGAGGCGATTGCCGATCTTATCGACGCCAGTTCGGAACAGGCGGCCCGTTCGGCAC  >  CP009273/3880148‑3880620

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑