Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,079,659	Δ1 bp	coding (1977/1992 nt)	tktA ←	transketolase 1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,079,656	0	T	.	96.2%	99.3 / ‑3.2	26	coding (1980/1992 nt)	tktA	transketolase 1
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base . (15/10);  total (16/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGCAAACGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTCTTTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAGCAGATTCAC  >  NC_000913/3079578‑3079729                                                                               |                                                                          ccGCAAACGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTCttt                                                                         >  1:507839/1‑81 (MQ=255) ccGCAAACGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTCttt                                                                         >  2:507847/1‑81 (MQ=255)       aCGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTc                                                                  >  1:507838/1‑81 (MQ=255)       aCGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTc                                                                  <  2:507816/81‑1 (MQ=255)            cATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGcaa                                                              >  1:507854/1‑80 (MQ=255)                  aaGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGtt                                                       <  1:507818/81‑1 (MQ=255)                     gTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTAt                                                     >  1:507869/1‑80 (MQ=255)                      taataaAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCa                                                   <  2:507818/81‑1 (MQ=255)                             aaaGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTg                                             >  2:507877/1‑80 (MQ=255)                             aaaGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTg                                             >  2:507844/1‑80 (MQ=255)                             aaaGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTT‑TTTTGCTTTCGCAACAACGTTATCAACAGTg                                             >  2:507852/1‑80 (MQ=255)                              aaGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGaa                                           <  1:507820/81‑1 (MQ=255)                                 gTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGcc                                        >  2:507820/1‑81 (MQ=255)                                       gAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAActc                                  >  2:507875/1‑81 (MQ=255)                                         aGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCtt                                <  1:507822/81‑1 (MQ=255)                                           cGACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAATAACGTTATCAACAGTGAAGCCGAACTCTTc                               >  2:507850/1‑80 (MQ=255)                                            gACCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCa                              >  1:507850/1‑80 (MQ=255)                                             aCCTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCaaa                            >  1:507859/1‑81 (MQ=255)                                               cTTTTTACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAAca                          <  2:507822/81‑1 (MQ=255)                                                  tttACCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAAcagc                        <  2:507823/80‑1 (MQ=255)                                                     acacGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACagcagc                     <  2:507824/77‑1 (MQ=255)                                                     aCCCGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGct                    >  2:507859/1‑81 (MQ=255)                                                       ccGAAATGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGctct                  >  1:507875/1‑81 (MQ=255)                                                          aaaTGCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGcc               >  2:507866/1‑81 (MQ=255)                                                              gCTAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAg           >  1:507872/1‑81 (MQ=255)                                                                tAATTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAg           >  1:507857/1‑79 (MQ=255)                                                                  aTTACAGCAGTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAGCAGa       <  2:507825/81‑1 (MQ=255)                                                                       agcagTTC‑TTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAGCAGATTCAc  <  2:507826/81‑1 (MQ=255)                                                                               |                                                                          CCGCAAACGGACATATCAAGGTAATAAAAAAGGTCGCCGAAGCGACCTTTTTACCCGAAATGCTAATTACAGCAGTTCTTTTGCTTTCGCAACAACGTTATCAACAGTGAAGCCGAACTCTTCAAACAGCAGCTCTGCCGGAGCAGATTCAC  >  NC_000913/3079578‑3079729

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑