Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	2,880,579	+A	76.7%	coding (1006/1053 nt)	pdxA ←	4‑hydroxythreonine‑4‑phosphate dehydrogenase

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	2,880,579	10	.→A	76.7%	19.1 0.0 ‑0.5	30	coding (1006/1053 nt)	pdxA	4‑hydroxythreonine‑4‑phosphate dehydrogenase
Reads supporting (aligned to +/- strand):  new base (21/2):  ref base (7/0):  total (28/2)
Fisher's exact test strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 3.26e-01

TCGCGCAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCC.CGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCGGG  >  NC_014034/2880479‑2880634                                                                                                      |                                                                  tCGCGCAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGAGCAGAGCCCCcggcg                                                                    <  2:787906/101‑1 (MQ=255)    cgcAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCggcg..........gcg                                                       >  2:2169254/1‑100 (MQ=255)    cgcAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCggcg..........gcg                                                       >  1:4333792/1‑100 (MQ=255)     gcAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCcggcg..........gagc                                                      >  1:587404/1‑98 (MQ=255)      cAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cg                                                    >  2:2896521/1‑101 (MQ=255)      cAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cg                                                    >  2:2391693/1‑101 (MQ=255)       aaGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgt                                                   >  2:795088/1‑100 (MQ=255)       aaGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgt                                                   >  1:3201459/1‑100 (MQ=255)         gggCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgtca                                                 >  2:2185637/1‑98 (MQ=255)          ggcggcAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgtcac                                                >  2:1042544/1‑97 (MQ=255)          ggcggcAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgtcac                                                >  1:545642/1‑97 (MQ=255)             ggcAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgtcacagc                                             >  1:1266681/1‑94 (MQ=255)               cAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgtcacagccg                                           >  2:1890414/1‑92 (MQ=25)                                                       cATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATc              >  2:3552354/1‑101 (MQ=9)                                                       cATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATc              >  2:2126126/1‑101 (MQ=9)                                                       cATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATc              >  2:2313433/1‑101 (MQ=9)                                                       cATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGGCAAGGCCGCGATc              >  2:3929105/1‑101 (MQ=2)                                                        ctCTTCCTTCAAATACCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCa             <  2:2120557/100‑1 (MQ=9)                                                        aTCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCa             >  1:1486681/1‑101 (MQ=9)                                                        aTCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCa             >  2:2872736/1‑101 (MQ=9)                                                         tCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATccg            >  2:2483284/1‑99 (MQ=9)                                                          cTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGa           >  1:2732462/1‑101 (MQ=9)                                                          cTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGa           >  2:1797565/1‑101 (MQ=9)                                                           ttGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGAc          >  2:2180277/1‑101 (MQ=9)                                                           ttGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGAc          >  1:3616674/1‑101 (MQ=9)                                                             gCTTCAAATATCCGGGGGGTCGGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACtg        <  1:2185776/101‑1 (MQ=12)                                                              cTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACtgt       >  1:2041846/1‑101 (MQ=12)                                                              cTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACtgt       >  2:3713978/1‑101 (MQ=12)                                                               ttCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACtgtg      >  1:704137/1‑101 (MQ=12)                                                               ttCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACtctg      >  2:1446721/1‑101 (MQ=9)                                                                tCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCCTCGTCAAGGCCGCGATCAGACTGTGc     >  1:1342240/1‑101 (MQ=9)                                                                 cAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGGCGCGATCAGACTGTGCg    >  2:4010299/1‑101 (MQ=9)                                                                 cAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCg    >  1:2577397/1‑101 (MQ=12)                                                                  aaaTATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCgg   >  1:1920837/1‑101 (MQ=12)                                                                  aaaTATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCgg   >  1:2788940/1‑101 (MQ=12)                                                                   aaTATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCggg  >  1:693873/1‑101 (MQ=12)                                                                                                      |                                                                  TCGCGCAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCC.CGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCGGG  >  NC_014034/2880479‑2880634 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG