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Detailed information for vg1000645768:

Variant ID: vg1000645768 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 645768
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.32, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


TTTACAACAATTACGGCAATAGATCGGCGGTGACGGTTGTCCGCACGTACTTTCTCCTCACTATTGTTCCTTCCTTGTGATCGCTACGTGAGTAAGGGGT[A/G]
TCTTCGTTTGATAGGAGGATGCTAGGGTCAACCGTCACCGTGAAAGGGGGTTGCCCATCAAACTGATCGTAATCCTCGTCAGTCTTGTCGTCTACTCCAA

Reverse complement sequence

TTGGAGTAGACGACAAGACTGACGAGGATTACGATCAGTTTGATGGGCAACCCCCTTTCACGGTGACGGTTGACCCTAGCATCCTCCTATCAAACGAAGA[T/C]
ACCCCTTACTCACGTAGCGATCACAAGGAAGGAACAATAGTGAGGAGAAAGTACGTGCGGACAACCGTCACCGCCGATCTATTGCCGTAATTGTTGTAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 18.90% 2.20% 25.41% 53.51% NA
All Indica  2759 1.30% 2.90% 32.48% 63.36% NA
All Japonica  1512 54.00% 0.70% 3.51% 41.87% NA
Aus  269 3.70% 3.70% 56.88% 35.69% NA
Indica I  595 1.50% 2.40% 36.97% 59.16% NA
Indica II  465 1.30% 0.90% 13.98% 83.87% NA
Indica III  913 0.90% 4.40% 39.65% 55.09% NA
Indica Intermediate  786 1.70% 2.70% 31.68% 63.99% NA
Temperate Japonica  767 87.40% 0.00% 0.52% 12.13% NA
Tropical Japonica  504 6.20% 2.00% 4.76% 87.10% NA
Japonica Intermediate  241 47.70% 0.00% 10.37% 41.91% NA
VI/Aromatic  96 9.40% 2.10% 81.25% 7.29% NA
Intermediate  90 25.60% 1.10% 23.33% 50.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000645768 A -> G LOC_Os10g02020.1 downstream_gene_variant ; 1512.0bp to feature; MODIFIER silent_mutation Average:11.299; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N
vg1000645768 A -> G LOC_Os10g02030.1 downstream_gene_variant ; 79.0bp to feature; MODIFIER silent_mutation Average:11.299; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N
vg1000645768 A -> G LOC_Os10g02020-LOC_Os10g02030 intergenic_region ; MODIFIER silent_mutation Average:11.299; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N
vg1000645768 A -> DEL N N silent_mutation Average:11.299; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000645768 NA 4.16E-07 mr1006 Jap_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
vg1000645768 NA 3.66E-07 mr1052 Jap_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
vg1000645768 NA 6.00E-15 mr1156 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
vg1000645768 NA 2.63E-06 mr1156 Jap_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
vg1000645768 NA 3.94E-09 mr1163 Jap_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
vg1000645768 NA 8.96E-08 mr1192 Jap_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
vg1000645768 NA 9.92E-06 mr1289 Jap_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
vg1000645768 NA 1.19E-06 mr1295 Jap_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
vg1000645768 9.10E-12 4.42E-32 mr1300 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
vg1000645768 NA 1.35E-08 mr1300 Jap_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
vg1000645768 4.94E-08 1.31E-42 mr1310 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
vg1000645768 NA 2.21E-08 mr1310 Jap_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
vg1000645768 NA 1.29E-06 mr1330 Jap_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
vg1000645768 NA 2.33E-07 mr1428 Jap_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
vg1000645768 NA 1.89E-10 mr1486 Jap_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
vg1000645768 NA 2.62E-08 mr1548 Jap_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
vg1000645768 NA 1.15E-07 mr1570 Jap_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
vg1000645768 NA 1.08E-11 mr1580 Jap_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
vg1000645768 NA 1.94E-09 mr1624 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
vg1000645768 NA 1.17E-07 mr1723 Jap_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
vg1000645768 NA 6.38E-06 mr1816 Jap_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
vg1000645768 NA 2.11E-10 mr1825 Jap_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
vg1000645768 NA 1.06E-09 mr1870 Jap_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
vg1000645768 2.97E-10 6.02E-50 mr1926 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
vg1000645768 NA 1.63E-09 mr1926 Jap_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
vg1000645768 1.13E-06 7.00E-13 mr1959 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
vg1000645768 NA 5.40E-06 mr1959 Jap_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
vg1000645768 6.00E-12 5.18E-44 mr1310_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
vg1000645768 6.80E-06 8.76E-13 mr1310_2 Jap_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
vg1000645768 NA 1.34E-09 mr1486_2 Jap_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
vg1000645768 NA 6.76E-09 mr1624_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
vg1000645768 1.66E-08 8.97E-20 mr1959_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
vg1000645768 NA 3.17E-09 mr1959_2 Jap_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