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Detailed information for vg0402256057:

Variant ID: vg0402256057 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2256057
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


GATGGTCATGGAACCACACAGGGAGGCGACCAGCATCCGTGTGCTGCTGTTGAAGGAGATGTAGGATGTCATGCTCCCCTCCAGTCTCGTGTTGCCGGGC[A/G]
AGACTGTTGAGTAGTTAGGCTCCCTAACAGAACTGATGCCGATGCAGATACGGTCGTTGCTAGTATCATTTTCGTAATTGTACGTGACGACGAACTCGAC

Reverse complement sequence

GTCGAGTTCGTCGTCACGTACAATTACGAAAATGATACTAGCAACGACCGTATCTGCATCGGCATCAGTTCTGTTAGGGAGCCTAACTACTCAACAGTCT[T/C]
GCCCGGCAACACGAGACTGGAGGGGAGCATGACATCCTACATCTCCTTCAACAGCAGCACACGGATGCTGGTCGCCTCCCTGTGTGGTTCCATGACCATC

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 39.20% 36.20% 3.26% 21.29% NA
All Indica  2759 24.20% 53.90% 4.13% 17.76% NA
All Japonica  1512 58.90% 10.00% 1.92% 29.17% NA
Aus  269 82.50% 3.00% 0.74% 13.75% NA
Indica I  595 6.90% 76.80% 5.21% 11.09% NA
Indica II  465 6.00% 75.90% 2.80% 15.27% NA
Indica III  913 44.70% 31.20% 2.96% 21.14% NA
Indica Intermediate  786 24.30% 49.90% 5.47% 20.36% NA
Temperate Japonica  767 88.30% 0.40% 0.13% 11.21% NA
Tropical Japonica  504 29.20% 25.20% 3.57% 42.06% NA
Japonica Intermediate  241 27.80% 8.70% 4.15% 59.34% NA
VI/Aromatic  96 30.20% 35.40% 7.29% 27.08% NA
Intermediate  90 48.90% 35.60% 2.22% 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
vg0402256057 A -> DEL LOC_Os04g04690.1 N frameshift_variant Average:51.18; most accessible tissue: Callus, score: 85.137 N N N N
vg0402256057 A -> G LOC_Os04g04690.1 missense_variant ; p.Leu173Ser; MODERATE nonsynonymous_codon ; L173S Average:51.18; most accessible tissue: Callus, score: 85.137 unknown unknown TOLERATED 0.10

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402256057 NA 5.25E-08 mr1037 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
vg0402256057 NA 4.90E-08 mr1068 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
vg0402256057 NA 1.34E-09 mr1108 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
vg0402256057 NA 5.83E-08 mr1111 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
vg0402256057 NA 9.23E-10 mr1112 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
vg0402256057 NA 6.61E-07 mr1181 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
vg0402256057 NA 6.41E-06 mr1187 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
vg0402256057 NA 7.82E-06 mr1212 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
vg0402256057 NA 2.50E-09 mr1234 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
vg0402256057 NA 4.33E-09 mr1237 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
vg0402256057 NA 5.67E-13 mr1270 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
vg0402256057 5.70E-06 9.13E-09 mr1285 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
vg0402256057 NA 3.08E-08 mr1403 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
vg0402256057 NA 5.26E-06 mr1432 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
vg0402256057 2.70E-06 NA mr1501 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
vg0402256057 3.19E-06 NA mr1523 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
vg0402256057 NA 2.42E-06 mr1568 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
vg0402256057 NA 8.56E-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
vg0402256057 NA 1.27E-13 mr1592 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
vg0402256057 NA 4.31E-08 mr1666 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
vg0402256057 NA 3.07E-08 mr1716 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
vg0402256057 NA 9.72E-09 mr1717 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
vg0402256057 NA 1.40E-07 mr1748 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
vg0402256057 NA 5.11E-11 mr1770 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
vg0402256057 9.88E-06 9.88E-06 mr1777 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
vg0402256057 NA 6.20E-08 mr1785 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
vg0402256057 2.00E-09 5.81E-54 mr1798 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
vg0402256057 NA 1.56E-09 mr1798 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
vg0402256057 NA 1.88E-07 mr1798 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
vg0402256057 NA 1.98E-08 mr1946 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
vg0402256057 NA 1.66E-06 mr1144_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