Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	2,880,579	+A	77.8%	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	77.8%	15.4 ‑2.2 ‑0.2	27	coding (1006/1053 nt)	pdxA	4‑hydroxythreonine‑4‑phosphate dehydrogenase
Reads supporting (aligned to +/- strand):  new base (20/1):  ref base (4/2):  total (24/3)
Fisher's exact test strand distribution p-value = 1.15e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 6.51e-01

TCGCGCAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCC.CGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCGGG  >  NC_014034/2880479‑2880634                                                                                                      |                                                                  tCGCGCAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCcggcg                                                                    >  2:785840/1‑101 (MQ=255)      caggggCGGAACCCCGTCAACCCCAGCCAAGGCCCGCCCCCTTCCTTTTCATCTTGCTTAAAATACCCGGGGGGTCGGGGGGCAGATCCCCCGGCG..........GCg.cg                                                    <  2:4802149/98‑1 (MQ=255)       aaGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgt                                                   >  1:2846674/1‑100 (MQ=255)       aaGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgt                                                   >  1:3697065/1‑100 (MQ=255)       aaGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgt                                                   >  2:2895368/1‑100 (MQ=255)            gggcACCCCGTCAACCGCAGCCAAACCCCGCCCCCTTCTTTTTCATTTTGCTTAAAATACCCCGGGGGCCGGGGGGCAGAGCCCCCGGCG..........GCg.cgtcacag                                              <  2:2275079/100‑7 (MQ=16)            cggcAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgtcacag                                              >  2:1886013/1‑95 (MQ=255)             ggcAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCCGCG..........GCg.cgtcacagc                                             >  1:3541917/1‑94 (MQ=25)               cAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCg.cgtcacagccg                                           >  1:1910507/1‑92 (MQ=25)                 gCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGCTCCGGGGGGAGAGCCCCCGGCG..........GCG.CGCAGccgcccgg                                         >  1:2168567/1‑98 (MQ=255)                                                   ttttCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCcgc                  >  2:3633399/1‑101 (MQ=2)                                                    tttCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCcgcg                 >  1:4804328/1‑101 (MQ=2)                                                      tCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGTGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGAt               >  1:4320577/1‑101 (MQ=9)                                                      tCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGAt               >  2:5118717/1‑101 (MQ=9)                                                      tCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGAt               >  2:187688/1‑101 (MQ=9)                                                      tCATCTTGCTTCAAATACCCCGGGGGCCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGAt               <  1:2629559/101‑1 (MQ=9)                                                       cATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATc              >  1:798018/1‑101 (MQ=9)                                                        aTCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGGGCGGCCCAGCCGCGCCGCCCCCCTCTTCGCCGCCCTCGTCAAGGCCGCGATCa             >  1:3916302/1‑101 (MQ=2)                                                        aTCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCa             >  1:4823257/1‑101 (MQ=9)                                                         tCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAg            >  1:1511547/1‑101 (MQ=9)                                                          cTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGa           >  2:4725230/1‑101 (MQ=9)                                                           ttGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGAc          >  2:3903674/1‑101 (MQ=9)                                                            tGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCCTCTTCGCCGCCATCGTCAAGGCCGCGATCAGACt         >  2:4162841/1‑101 (MQ=9)                                                            tGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACt         >  2:5330819/1‑101 (MQ=9)                                                              cTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGGCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACtgt       >  1:4223589/1‑101 (MQ=9)                                                               ttCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCCCAGCCGCGCCGCCCCCATCTTCGCCGCCCTCGTCAAGGCCGCGATCAGACtggg      >  1:5652502/1‑99 (MQ=9)                                                               ttCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACtgtg      >  2:2535515/1‑101 (MQ=12)                                                               ttCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACtgtg      >  2:988048/1‑101 (MQ=12)                                                                tCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGc     >  1:5485522/1‑101 (MQ=12)                                                                 cAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCg    >  2:3718286/1‑101 (MQ=12)                                                                 cAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCg    >  1:5337774/1‑101 (MQ=12)                                                                  aaaTATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCgg   >  1:5394219/1‑101 (MQ=12)                                                                   aaTATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGCCGCGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGGGCggg  >  2:1047901/1‑101 (MQ=12)                                                                                                      |                                                                  TCGCGCAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCC.CGCCGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCGGG  >  NC_014034/2880479‑2880634 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG