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Detailed information for vg0801799521:

Variant ID: vg0801799521 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 1799521
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGGAAAATTTGTGAGTGGAATTGGCGGCGGCAGCGAACCTCGTATCGTGTGCCGCCCCGGCCTCCACCCCTGTTTATATGGCACGGGGTGACGGGGGCC[T/C]
ACCAGCCAATGGGCTGGGCGCCCTCGATCAGGGCGCGGGTCAAGGTCCCCTTGTGCCGTTGGGCTCAAGGGGGAGAGAGATCTATCAAACATCCATTTGT

Reverse complement sequence

ACAAATGGATGTTTGATAGATCTCTCTCCCCCTTGAGCCCAACGGCACAAGGGGACCTTGACCCGCGCCCTGATCGAGGGCGCCCAGCCCATTGGCTGGT[A/G]
GGCCCCCGTCACCCCGTGCCATATAAACAGGGGTGGAGGCCGGGGCGGCACACGATACGAGGTTCGCTGCCGCCGCCAATTCCACTCACAAATTTTCCTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.90% 31.80% 0.49% 17.73% NA
All Indica  2759 48.40% 23.00% 0.65% 27.98% NA
All Japonica  1512 59.10% 40.70% 0.07% 0.13% NA
Aus  269 1.10% 78.10% 1.49% 19.33% NA
Indica I  595 68.40% 28.10% 0.00% 3.53% NA
Indica II  465 76.80% 14.00% 0.22% 9.03% NA
Indica III  913 15.20% 22.80% 1.20% 60.79% NA
Indica Intermediate  786 54.80% 24.80% 0.76% 19.59% NA
Temperate Japonica  767 97.00% 2.90% 0.13% 0.00% NA
Tropical Japonica  504 11.10% 88.50% 0.00% 0.40% NA
Japonica Intermediate  241 39.00% 61.00% 0.00% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 51.10% 35.60% 0.00% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0801799521 T -> C LOC_Os08g03770.1 upstream_gene_variant ; 4635.0bp to feature; MODIFIER silent_mutation Average:54.559; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0801799521 T -> C LOC_Os08g03790.1 upstream_gene_variant ; 262.0bp to feature; MODIFIER silent_mutation Average:54.559; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0801799521 T -> C LOC_Os08g03780.1 downstream_gene_variant ; 305.0bp to feature; MODIFIER silent_mutation Average:54.559; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0801799521 T -> C LOC_Os08g03780-LOC_Os08g03790 intergenic_region ; MODIFIER silent_mutation Average:54.559; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0801799521 T -> DEL N N silent_mutation Average:54.559; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0801799521 NA 2.66E-06 mr1177 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
vg0801799521 NA 2.50E-11 mr1180 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
vg0801799521 NA 4.35E-13 mr1183 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
vg0801799521 NA 2.60E-07 mr1229 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
vg0801799521 NA 4.87E-13 mr1503 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
vg0801799521 NA 1.13E-07 mr1671 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
vg0801799521 5.19E-12 9.80E-24 mr1739 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
vg0801799521 6.08E-12 5.23E-25 mr1739 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
vg0801799521 NA 1.55E-10 mr1880 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
vg0801799521 NA 4.41E-06 mr1942 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
vg0801799521 NA 6.58E-10 mr1047_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
vg0801799521 NA 3.97E-06 mr1077_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
vg0801799521 NA 1.58E-08 mr1156_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
vg0801799521 NA 3.20E-13 mr1189_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
vg0801799521 NA 5.28E-06 mr1206_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
vg0801799521 NA 7.19E-07 mr1229_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
vg0801799521 NA 1.92E-06 mr1295_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
vg0801799521 NA 1.05E-11 mr1338_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
vg0801799521 NA 2.68E-07 mr1338_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
vg0801799521 NA 9.34E-10 mr1350_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
vg0801799521 NA 2.32E-08 mr1378_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
vg0801799521 NA 7.24E-06 mr1397_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
vg0801799521 NA 9.17E-06 mr1425_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
vg0801799521 NA 1.57E-06 mr1428_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
vg0801799521 NA 5.55E-07 mr1483_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
vg0801799521 NA 6.88E-06 mr1498_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
vg0801799521 NA 3.87E-16 mr1530_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
vg0801799521 NA 1.00E-05 mr1596_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
vg0801799521 NA 6.02E-06 mr1621_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
vg0801799521 NA 9.86E-06 mr1654_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
vg0801799521 NA 3.25E-07 mr1722_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
vg0801799521 1.15E-07 9.37E-23 mr1739_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
vg0801799521 NA 9.70E-19 mr1739_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
vg0801799521 NA 6.79E-17 mr1794_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
vg0801799521 NA 6.19E-07 mr1807_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
vg0801799521 NA 9.34E-09 mr1815_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
vg0801799521 NA 1.76E-09 mr1864_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
vg0801799521 NA 2.59E-10 mr1952_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
vg0801799521 NA 9.59E-07 mr1966_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