Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,080,006	T→C	11.8%	K544E (AAA→GAA)	tktA ←	transketolase 1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,080,006	0	T	C	11.8%	74.4 / 4.1	34	K544E (AAA→GAA)	tktA	transketolase 1
Reads supporting (aligned to +/- strand):  ref base T (17/13);  new base C (2/2);  total (19/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.25e-02

CAAATGCGTCGGTAGACGGCATGGACACCACGCGCGCTTTCACGCCTTCGGCAGTCAGTTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACCGCGGATTCAA  >  NC_000913/3079868‑3080146                                                                                                                                           |                                                                                                                                             cAAATGCGTCGGTAGACGGCATGGACACCACGCGCGCTTTCACGCCTTCGGCAGTCAGTTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGc                                                                                                                                          <  1:273223/143‑1 (MQ=255)  aaaTGCGTCGGTAGACTGCATCGACATCGCGCGCGCTTTCACGCCTTCGGCAGTCAGTTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGca                                                                                                                                         <  2:398257/143‑1 (MQ=255)        gTCGGTAGACGGCATGGACACCACGCGCGCTTTCACGCCTTCGGCAGTCAGTTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAac                                                                                                                                   >  1:479400/1‑143 (MQ=255)            gTAGACGGCATGGACACCACGCGCGCTTTCACGCCTTCGGCCGTCAGTTTTTCGTAGGAAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAAACAGTTCCGGCTGACCGGCGCAGTATGTCAGCAAAGAaacaca                                                                                                                               >  2:600876/1‑142 (MQ=255)                         ccaccacGCGCGCTTTCACGCCTTCGGCAGTCAGTTTGTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGttt                                                                                                                  <  1:324017/142‑1 (MQ=255)                             cacGCGCGCTTTCACGCCTTCGGCAGTCAGTTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGGGATGAAACTCAGTTCCGGCTGACCGGCGCCGTCTTTCAGCACATCACCACCGCGCGCGCTGTGTGccg                                                                                                              >  2:114295/1‑142 (MQ=255)                              acGCGCGCTTTCACGCCTTCGGCAGTCAGTTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGACCCGGTAGCGATGAACATAAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACAACGCGCACAGTTTGCCAg                                                                                                             >  1:373402/1‑143 (MQ=255)                              acGCGCGCTTTCACGCCTTCGGCAGTCAGTTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCCTTCAGCACATAACCACCGCGCGCGATGTTTGCCAg                                                                                                             >  1:156523/1‑143 (MQ=255)                                gcgcgcTTTCACGCCTTCGGCAGGCAGTTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGCTGAAAATCAGTTCCGGCTGACCGGCCCAAGCTTTCCGCACATAACCACCCCGCGCGATGCTTGCCacgt                                                                                                           >  2:605947/1‑140 (MQ=255)                                    gcTTTCACGCCTTCGGCAGTCAGTTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCCCGATGTTTGCCTGTTGctc                                                                                                       >  1:594866/1‑143 (MQ=255)                                           cGCCGTCGGCAGTCAGTTGTGCGTAGGCAGCAACAGCCAGTTCGACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAgtt                                                                                                <  1:279634/143‑1 (MQ=255)                                                  ggCAGTCAGTTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCct                                                                                         <  1:82478/143‑1 (MQ=255)                                                   gCAGTCAGTGTTTGGTCGGCAGCAACAGCCAGTTCAACCTCTGACCCGGTAGCGATGAAAATCAGTTCCGGCTGGCGGGCGCAGTCTGTCAGCACATACCCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCctg                                                                                        <  2:153839/143‑1 (MQ=255)                                                          gtTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGGTCGGTCCTGCTGCGcc                                                                                 >  1:180615/1‑143 (MQ=255)                                                             tttCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGAAGTTTGCCAGTTGCCCTTCAGTTCGCTCCTGCTGCGCCAgg                                                                              >  2:382365/1‑143 (MQ=255)                                                             tttCGTAGGCAGCAACAGCCAGAACAACTTCTGAACCGGTACCGACGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAgg                                                                              <  1:90957/143‑1 (MQ=255)                                                                cGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTc                                                                           <  1:339697/143‑1 (MQ=255)                                                                      cagcaAGAGCCAGTTAAACTTCTGAGCCGGTAGCGATGAAAATCAGTCCCGGCTGGCCGGCGCAGTCTTTCAGCACATATCCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAATACGTGCTGGTGGCGCCAGGTTCTGACgg                                                                     <  2:408885/143‑1 (MQ=255)                                                                           aCAGCAAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGagag                                                                <  2:517070/143‑1 (MQ=255)                                                                              gCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCCCCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGAt                                                             <  1:223745/143‑1 (MQ=255)                                                                                   ttCAACTTCTGAACAGGTAGCGATGAAAATCAGGTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGAGCGCGATGGTTGCCAGTTGCTCTTCAGGTCGTTCCTGCTGCGCCCGGTTCTGGCGGGAGGGGATCAGTg                                                        >  1:643404/1‑143 (MQ=255)                                                                                      aaCTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGCCGGGAGCAGTCTTTGAGCACATAACCACCGCGCGCGATGTTTGCCCGTTGCTCTTCACTTCGTTACTGCTGCGCCCGGTTCTGACGGGAGAGGATAAGTGCgc                                                     >  2:366769/1‑142 (MQ=255)                                                                                      aaCTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTCCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCgg                                                     >  1:468094/1‑143 (MQ=255)                                                                                      aaCTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTCCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCgg                                                     >  1:466039/1‑143 (MQ=255)                                                                                          tCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTCCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCgg                                                 <  2:466039/143‑1 (MQ=255)                                                                                          tCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTCCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCgg                                                 <  2:468094/143‑1 (MQ=255)                                                                                           cTGCACCGGTAGCGATGAAACTCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGAGGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCggg                                                <  1:76701/143‑1 (MQ=255)                                                                                            ggAACCGGTCGCGATGAAACTCAGTTCCGGCCGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGc                                               <  1:240293/142‑1 (MQ=255)                                                                                              aaCCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCg                                             >  1:645263/1‑143 (MQ=255)                                                                                                        gATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTGGACAGTTCCTCTTCAGTTCGTTCCCGCTGCGCCAGGTTCTGACGGGAGAGGAGCAGTGCGGCCGGGCGGTCCTgcggct                                   >  2:529424/1‑138 (MQ=255)                                                                                                            aaaaTCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAac                               >  2:195712/1‑143 (MQ=255)                                                                                                                           tGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACCCTCAACACCCTCTTTCCAcgc                >  2:454622/1‑143 (MQ=255)                                                                                                                               cGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGCTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGAGGCTCAACACCGTATTTACACGCGAca            >  1:140259/1‑142 (MQ=255)                                                                                                                                 gcgcAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACcgc          >  1:411051/1‑143 (MQ=255)                                                                                                                                         tttCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGGTCTGACGGGAGAGGATCAGTGCGGTAGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGGCCGCGGagccaa  >  2:561418/1‑138 (MQ=255)                                                                                                                                         tttCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTGCAGTTCGTTCCTGCTGCGCCAAGTTCTGACGGGCGGGGGTCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTCTTTGCACGAGCCCGCGGATTCaa  >  1:618555/1‑143 (MQ=255)                                                                                                                                         cttCAGCCCATAACCGCCTCGCGCGATGTGTTCCAGTTGCTCTTCAGTGCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACCGCGGATTCaa  <  2:479400/142‑1 (MQ=255)                                                                                                                                           |                                                                                                                                             CAAATGCGTCGGTAGACGGCATGGACACCACGCGCGCTTTCACGCCTTCGGCAGTCAGTTTTTCGTAGGCAGCAACAGCCAGTTCAACTTCTGAACCGGTAGCGATGAAAATCAGTTCCGGCTGACCGGCGCAGTCTTTCAGCACATAACCACCGCGCGCGATGTTTGCCAGTTGCTCTTCAGTTCGTTCCTGCTGCGCCAGGTTCTGACGGGAGAGGATCAGTGCGGTCGGGCCGTCCTGACGCTCAACACCGTATTTCCACGCGACCGCGGATTCAA  >  NC_000913/3079868‑3080146

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑