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Detailed information for vg1008541700:

Variant ID: vg1008541700 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 8541700
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


CATTTCCATTCCTGGATTTGAAGAGGTTGGAGTAAACCTGCTGGTCTTTGGTGCTCTGCCTTCACTCGTTGACAAACATCGCAGAGTACGACGAATTCAG[C/G]
TATTTCTCTCCTCATGCTGACCCACCAAAACTTTTCTTTGAGGTCTTGATACATTTTGGTGCTGCCTGGATGAATGGAGTACTGGGTCTGATGAGCCTCG

Reverse complement sequence

CGAGGCTCATCAGACCCAGTACTCCATTCATCCAGGCAGCACCAAAATGTATCAAGACCTCAAAGAAAAGTTTTGGTGGGTCAGCATGAGGAGAGAAATA[G/C]
CTGAATTCGTCGTACTCTGCGATGTTTGTCAACGAGTGAAGGCAGAGCACCAAAGACCAGCAGGTTTACTCCAACCTCTTCAAATCCAGGAATGGAAATG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.40% 20.90% 25.41% 14.33% NA
All Indica  2759 38.40% 34.80% 23.52% 3.26% NA
All Japonica  1512 48.30% 0.70% 17.33% 33.60% NA
Aus  269 2.60% 0.40% 75.84% 21.19% NA
Indica I  595 9.70% 86.60% 2.02% 1.68% NA
Indica II  465 60.40% 17.00% 15.91% 6.67% NA
Indica III  913 41.80% 14.70% 42.72% 0.77% NA
Indica Intermediate  786 43.00% 29.60% 22.01% 5.34% NA
Temperate Japonica  767 55.00% 0.70% 2.35% 41.98% NA
Tropical Japonica  504 32.90% 0.80% 42.46% 23.81% NA
Japonica Intermediate  241 59.30% 0.80% 12.45% 27.39% NA
VI/Aromatic  96 26.00% 0.00% 60.42% 13.54% NA
Intermediate  90 44.40% 14.40% 31.11% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1008541700 C -> G LOC_Os10g17050.1 missense_variant ; p.Ala1088Pro; MODERATE nonsynonymous_codon ; A1088P Average:20.662; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 probably damaging 2.39 DELETERIOUS 0.00
vg1008541700 C -> DEL LOC_Os10g17050.1 N frameshift_variant Average:20.662; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1008541700 1.73E-09 2.86E-39 mr1026 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 8.49E-10 7.39E-21 mr1026 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 2.24E-06 NA mr1110 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 5.25E-06 mr1113 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 1.89E-06 mr1114 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 8.12E-09 6.59E-19 mr1118 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 1.13E-12 9.38E-23 mr1118 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 9.10E-09 8.23E-37 mr1161 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 2.05E-09 1.44E-19 mr1161 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 6.23E-08 8.85E-24 mr1495 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 6.63E-10 1.54E-24 mr1495 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 2.98E-06 2.82E-11 mr1496 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 8.85E-06 mr1789 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 2.41E-10 mr1794 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 8.52E-06 mr1936 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 7.86E-08 3.39E-23 mr1118_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 3.73E-13 4.76E-30 mr1118_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 8.86E-07 mr1120_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 1.16E-07 mr1123_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 9.65E-12 3.07E-42 mr1161_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 5.69E-11 8.24E-24 mr1161_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 7.97E-07 mr1242_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 1.03E-08 2.12E-31 mr1495_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 6.92E-11 1.14E-29 mr1495_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 1.43E-11 mr1496_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 3.95E-07 mr1531_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 5.95E-06 NA mr1580_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 6.72E-07 6.86E-07 mr1580_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 3.56E-13 mr1794_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 2.05E-06 NA mr1825_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 2.09E-07 2.81E-07 mr1825_2 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 1.45E-06 mr1870_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 NA 2.99E-07 mr1904_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1008541700 9.83E-06 2.26E-11 mr1936_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251