Predicted mutation | |||||||
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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... | ||||||||||
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seq id | position | change | freq | score | reads | annotation | genes | product | ||
* | NC_014034 | 2,880,579 | 10 | .→A | 73.1% | 19.6 ‑4.3 ‑0.1 | 26 | coding (1006/1053 nt) | pdxA | 4‑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
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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)
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CGCGCAAGGGCGGCAGCCCGTCAATCGCAGCCAAAGCCCGTCCCCTTCCTTTTCATCTTGCTTCAAATATCCCGGGGGTCCGGGGGCAGAGCCCCCGGCG..........GC.........C..CGC..CGCCCCCATCTTCGCCGCCATCGTCAAGGCCGCGATCAGACTGTGCGGGC > NC_014034/2880480‑2880635
Base quality scores: 
ATCG
< 3 ≤
ATCG
< 15 ≤
ATCG
< 23 ≤
ATCG
< 33 ≤
ATCG
< 40 ≤
ATCG
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