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Detailed information for vg0604294396:

Variant ID: vg0604294396 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4294396
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


CGTACTCATCCAGAAGCATTTCATAGCTGTCAGCCACAGAGTGACCCTGATCTGCCATCTCTTAAAATGCACACCGGTGAATTTATCCGGCCTCAGTGCA[C/T]
CGGCAAAACCAGCCATAGTAAAATCACAGTGCCTATAATAAGGTTTTTTGGATTGTTGAGATTATGGGCATATAATGATTTAATTTATTCCATAAATAAA

Reverse complement sequence

TTTATTTATGGAATAAATTAAATCATTATATGCCCATAATCTCAACAATCCAAAAAACCTTATTATAGGCACTGTGATTTTACTATGGCTGGTTTTGCCG[G/A]
TGCACTGAGGCCGGATAAATTCACCGGTGTGCATTTTAAGAGATGGCAGATCAGGGTCACTCTGTGGCTGACAGCTATGAAATGCTTCTGGATGAGTACG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 12.70% 0.60% 1.59% 85.12% NA
All Indica  2759 1.10% 0.80% 1.09% 96.96% NA
All Japonica  1512 37.20% 0.10% 2.05% 60.65% NA
Aus  269 0.00% 0.40% 1.86% 97.77% NA
Indica I  595 0.70% 1.00% 0.17% 98.15% NA
Indica II  465 1.10% 1.30% 0.43% 97.20% NA
Indica III  913 0.30% 0.10% 0.99% 98.58% NA
Indica Intermediate  786 2.40% 1.30% 2.29% 94.02% NA
Temperate Japonica  767 63.80% 0.00% 2.61% 33.64% NA
Tropical Japonica  504 3.20% 0.00% 1.39% 95.44% NA
Japonica Intermediate  241 24.10% 0.40% 1.66% 73.86% NA
VI/Aromatic  96 0.00% 1.00% 6.25% 92.71% NA
Intermediate  90 8.90% 0.00% 3.33% 87.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0604294396 C -> T LOC_Os06g08630.1 missense_variant ; p.Gly6Asp; MODERATE nonsynonymous_codon ; G6D Average:5.011; most accessible tissue: Zhenshan97 young leaf, score: 7.417 unknown unknown TOLERATED 1.00
vg0604294396 C -> DEL LOC_Os06g08630.1 N frameshift_variant Average:5.011; most accessible tissue: Zhenshan97 young leaf, score: 7.417 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604294396 4.28E-14 3.83E-35 mr1115 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
vg0604294396 2.92E-12 3.65E-29 mr1115 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
vg0604294396 1.90E-27 4.34E-62 mr1137 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
vg0604294396 7.39E-13 2.00E-21 mr1137 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
vg0604294396 NA 5.24E-11 mr1241 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
vg0604294396 NA 9.66E-09 mr1552 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
vg0604294396 NA 3.03E-06 mr1576 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
vg0604294396 1.41E-09 2.24E-30 mr1611 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
vg0604294396 8.94E-07 7.64E-19 mr1611 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
vg0604294396 2.91E-23 3.17E-51 mr1617 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
vg0604294396 4.06E-11 2.47E-16 mr1617 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
vg0604294396 8.43E-12 6.14E-32 mr1920 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
vg0604294396 5.36E-08 3.39E-18 mr1920 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
vg0604294396 1.10E-12 2.40E-36 mr1115_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
vg0604294396 1.51E-10 7.43E-28 mr1115_2 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
vg0604294396 1.76E-23 9.92E-61 mr1137_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
vg0604294396 3.00E-11 5.40E-18 mr1137_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
vg0604294396 3.42E-08 NA mr1241_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
vg0604294396 NA 4.10E-15 mr1241_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
vg0604294396 2.93E-08 1.06E-29 mr1611_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
vg0604294396 1.94E-07 3.62E-20 mr1611_2 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
vg0604294396 5.69E-13 1.47E-38 mr1617_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
vg0604294396 6.38E-07 8.50E-11 mr1617_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
vg0604294396 NA 2.87E-06 mr1680_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