Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_pae_tpiA	3,528,907	A→T	24.1%	D80V (GAT→GTT)	yrfG →	GMP/IMP nucleotidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	3,528,907	0	A	T	24.1%	51.9 / 8.7	32	D80V (GAT→GTT)	yrfG	GMP/IMP nucleotidase
Reads supporting (aligned to +/- strand):  ref base A (14/10);  new base T (2/6);  total (16/16)
Fisher's exact test for biased strand distribution p-value = 2.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGCAAAAGCTGGTGCCTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTGGCGGTAAAACTTGAG  >  NC_000913_3_pae_tpiA/3528759‑3529052                                                                                                                                                     |                                                                                                                                                  tGGCAAAAGCTGGTGCCGGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGGTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGa                                                                                                                                                   <  2:441230/149‑1 (MQ=255)      aaaGCTGGTGCCTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGCATATATGCGCCAGCAATATCACGGCGTAAATCATTCGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGatattt                                                                                                                                              >  1:350722/1‑147 (MQ=255)      aaaGCTGGTGCCTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCGGGTTGTCt                                                                                                                                              >  1:274471/1‑149 (MQ=255)            ggTGCCTGAAAGATGGGGCGCGAAAACCGGGGTTACGCCACAGGAAGCGTTGGGATATATGCGCCAGCAATATCACGACGTACAGCAGACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGa                                                                                                                                        <  1:464986/149‑1 (MQ=255)             gTGCCTGAAACATGGGGCGCGAAAAACGGGGTTGCGCCACAGGAAGCGATGGAATATATGCGCCGGCAATGTTACGACGTACAGCATACGCTAAACTGGTACTGTCTTTATTACTGGAGTGAGCAACGGGGTCTGGTTATCtttacgtt                                                                                                                                       >  2:160384/1‑142 (MQ=255)              tGCCTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATg                                                                                                                                      >  1:645096/1‑149 (MQ=255)                 cTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGacc                                                                                                                                   >  2:177824/1‑149 (MQ=255)                  tGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGacca                                                                                                                                  >  1:448556/1‑149 (MQ=255)                       cATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGGGAGCAACTGGGTCTGGAGATCTGTGCGATGACCACCcag                                                                                                                             >  1:391964/1‑149 (MQ=255)                        aTGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCgaga                                                                                                                            >  1:122451/1‑149 (MQ=255)                                         gggTTCCTCCACCGGAAGCGATGGAATATATGCGCCAGCATTCTGACGACGTACAGCATACGCTACACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTTTTTTTAATGCTGCGGCGACCACCTATATGGTACCGCGTGCCGtc                                                                                                           <  2:581887/149‑2 (MQ=255)                                         gggTTACGCCACAGGAAGCGATGGAATGTATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTa                                                                                                           <  1:378386/149‑1 (MQ=255)                                          ggTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACTACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTTTTTTTTTTTAATGATGCGGCGACCACCGAGATGGGACCGCGTGCCGTAc                                                                                                          <  2:721698/149‑1 (MQ=255)                                                  cacaGTAAGCGATGGTATATGTGCGCTCGCATTACCACGACGGATCGCATACGCTATATTGGTACTGTGTTGATTCCTGGAGTGAGCAACTTGGTTTTTTTATTGGTGCGGCGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGaa                                                                                                  <  2:461466/149‑1 (MQ=255)                                                       gAAGCGGTTGCATATGTGCGCCAGGAATATCGACATGTAGAGCATATGCTACACTTGTACTGTTTTGATGACGGGAGTGATCAATTTGTTTTTTTTAATGATACGGTGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATAc                                                                                             <  2:412436/149‑1 (MQ=255)                                                                   tatatGGTCCATCAATATAACGACGTACATCATACGTGAAACTGTGAATGACTTGATTACTGGAGTGGGCTACTTTTTTTTTTTAATGATACGGCGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCt                                                                                 <  2:162444/149‑1 (MQ=255)                                                                      atGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGa                                                                              >  1:288050/1‑149 (MQ=255)                                                                                      acgacgTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTGTTGAGGCACTGAAAGCCAGc                                                              >  1:82428/1‑149 (MQ=255)                                                                                              ccgCATACGCTAATCTGGTACTGTCTTGATTACTGGAGTGATCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAagca                                                      <  1:202683/147‑1 (MQ=255)                                                                                                gCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCTTGCCGTACTAAGAAACGATAGGATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAagcagc                                                    <  1:726644/149‑1 (MQ=255)                                                                                                             tGGTACTGTCGTGTTTCCTGGTGTGAGCAAGTTGTTTTTTTTAATGATGCGGCGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGCTACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCAc                                       <  2:708634/149‑1 (MQ=255)                                                                                                                tACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGCTTCTTGAGGCACTGAAAGCCAGCGGTAGGCAGCGAGTTTTGCTccccca                                    >  1:16896/1‑147 (MQ=255)                                                                                                                       ttGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGGTGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTACCTTGAGGCACTAAAAGACAGAGGTAAGCAGCGACTATTGCCCGCCAATgtacat                             >  2:126123/1‑144 (MQ=255)                                                                                                                       ttGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCAt                             >  1:259781/1‑149 (MQ=255)                                                                                                                       ttGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCATGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCAt                             >  1:694384/1‑149 (MQ=255)                                                                                                                          aTTACTGGAGTGAGCAGCGGGGTCGGGAGCTCTGCGCGATGCCCACCGAGAGGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCg                          <  1:708597/149‑1 (MQ=255)                                                                                                                           ttACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGTAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGc                         <  1:674491/149‑1 (MQ=255)                                                                                                                              cTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGcaca                      >  1:386746/1‑149 (MQ=255)                                                                                                                                 gAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCACACAAcc                   >  1:646041/1‑149 (MQ=255)                                                                                                                                  aGTGAGCAACTTGTTCTGTATAACTGTGCGGTGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCt                  <  2:732867/149‑1 (MQ=255)                                                                                                                                   gTGCGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTg                 <  1:419810/149‑1 (MQ=255)                                                                                                                                     gAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTGGc               <  1:177824/149‑1 (MQ=255)                                                                                                                                        cAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTGGCGGt            >  1:419069/1‑149 (MQ=255)                                                                                                                                                  tGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTGGCGGTAAAACTTGAg  <  1:23627/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                  TGGCAAAAGCTGGTGCCTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTGGCGGTAAAACTTGAG  >  NC_000913_3_pae_tpiA/3528759‑3529052

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: ‑