Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_014034 2,880,579 +A 73.1% coding (1006/1053 nt) pdxA ← 4‑hydroxythreonine‑4‑phosphate dehydrogenase

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*NC_0140342,880,57910.→A73.1% 19.6 ‑4.3 ‑0.126coding (1006/1053 nt)pdxA4‑hydroxythreonine‑4‑phosphate dehydrogenase
Reads supporting (aligned to +/- strand):  new base (19/0):  ref base (4/3):  total (23/3)
Fisher's exact test strand distribution p-value = 1.35e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 7.93e-01

CGCGCAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GC.........C..CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCGGGC  >  NC_014034/2880480‑2880635
                                                                                                    |                                                                              
cgcgCAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCcggcg..........g                                                                      >  2:2955871/1‑101 (MQ=255)
   gcAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCggcg..........gcgc                                                                   >  2:4128286/1‑99 (MQ=255)
     aaGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCcggcg..........gagggc                                                                 >  1:55374/1‑96 (MQ=255)
     aaGGGCGGCAGCACGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCggcg..........gcggct                                                                 >  1:2573453/1‑97 (MQ=255)
      aGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCTTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCcggcg..........gggggtc                                                                >  1:1096838/1‑95 (MQ=255)
        ggcggcAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GC.........g..cgtcac                                                   >  1:2053843/1‑97 (MQ=255)
        ggcggcAGCCCGTCAACCGCACCCAAAGCCCGCCCCCTTCCTTTTCATCTTTCTTCAAATATCCGGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GC.........g..cgtcac                                                   <  2:2985499/101‑5 (MQ=25)
         gcggcAGCCCTTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATACCCGGGGGGTCCGGGGGCAGACCCCCCGGCG..........GC.........g..cgtcaca                                                  <  2:4514289/101‑6 (MQ=25)
         ctggcCGCCCCTCACCCGCAGCGAAGGCCCGCCCCCTACCTTTTCATCTTGCTTCAAATTTCCGGGGGGTCCGGGGGGAGAACCCCCGGCG..........GC.........g..cgtcaca                                                  <  2:3098333/99‑6 (MQ=255)
          cggcAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCCCCG..........GC.........g..cgtcacag                                                 >  2:4207800/1‑95 (MQ=25)
            gcAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GC.........g..cgtcacagcc                                               >  1:1997346/1‑93 (MQ=255)
             cAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GC.........g..cgtcacagccg                                              >  1:4159063/1‑92 (MQ=25)
                                                 ttttCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCcgc                   >  2:4501785/1‑101 (MQ=2)
                                                  tttCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCcgcg                  >  1:1037891/1‑101 (MQ=2)
                                                  tttCATCTTGCTTCAAATATCCCGGGGGCCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCcgcg                  >  2:527606/1‑101 (MQ=2)
                                                    tCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGAt                >  2:123905/1‑101 (MQ=9)
                                                    tCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGAt                >  2:3495523/1‑101 (MQ=9)
                                                       tCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAg             >  1:4722093/1‑101 (MQ=9)
                                                         ttGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGGGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCCCCGCCATCGTCAAGGCCGCGATCCGAc           >  2:2821630/1‑101 (MQ=9)
                                                         ttGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCCTCTTCGCCGCCCTCGTCAAGGCCGCGATCAGAc           >  1:2382809/1‑101 (MQ=9)
                                                          tGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACt          >  2:3135307/1‑101 (MQ=9)
                                                          tGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACt          >  2:4634201/1‑101 (MQ=9)
                                                            cTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACtgt        >  1:547718/1‑101 (MQ=12)
                                                            cTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGCCAAGGCCGCGATCAGACtga        >  1:1236281/1‑100 (MQ=9)
                                                             ttCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGatcaga       >  2:2840661/1‑96 (MQ=9)
                                                              tCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGc      >  1:3379932/1‑101 (MQ=12)
                                                              tCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCACCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGc      >  2:4729504/1‑101 (MQ=9)
                                                                aaaTATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCgg    >  2:2475196/1‑101 (MQ=12)
                                                                aaaTATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCgg    >  2:3956869/1‑101 (MQ=12)
                                                                aaaTATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGGCACAGC.........CG.CGC..CGCCCCCCTCTTCGCCGCCATCGTCAAGGCCGCCATCAAACTGTGCgg    >  2:3251469/1‑101 (MQ=2)
                                                                aaaTATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCGCGGCACAGC..CGCGGCGGCCCCATCTTCGCCGCCCTCGTCAAGGCCGCGCTCAGACTGCGCgg    >  2:129286/1‑101 (MQ=2)
                                                                 aaTATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCggg   >  1:3887630/1‑101 (MQ=12)
                                                                 aaTATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCGGCGCGTCACAGC.........CG.CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCggg   >  2:1398853/1‑101 (MQ=12)
                                                                  atatCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GCGCGTCACAGCCGCGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCGGGc  >  1:1326942/1‑101 (MQ=12)
                                                                                                    |                                                                              
CGCGCAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GC.........C..CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCGGGC  >  NC_014034/2880480‑2880635

Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 23 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG