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Detailed information for vg1124304377:

Variant ID: vg1124304377 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24304377
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


GCATTGAAGTTGGCACTAAATAGATGAATTCATAAATATGGAAATTTCCCGACCGTTTCTGTTCGTTTTCCAAAAAAATAATAAAATAATGTACTGTTTC[C/T]
GACCATTTCCGACCGTTTTCATCCCTATCCATGGGGGAGTACTGGGTTCGTACCCACTGAACACGTATCTTAATACTAAATGACAGGTTTTAAACTGAAA

Reverse complement sequence

TTTCAGTTTAAAACCTGTCATTTAGTATTAAGATACGTGTTCAGTGGGTACGAACCCAGTACTCCCCCATGGATAGGGATGAAAACGGTCGGAAATGGTC[G/A]
GAAACAGTACATTATTTTATTATTTTTTTGGAAAACGAACAGAAACGGTCGGGAAATTTCCATATTTATGAATTCATCTATTTAGTGCCAACTTCAATGC

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 69.10% 29.30% 1.65% 0.00% NA
All Indica  2759 53.60% 44.00% 2.39% 0.00% NA
All Japonica  1512 97.80% 2.10% 0.13% 0.00% NA
Aus  269 69.10% 29.70% 1.12% 0.00% NA
Indica I  595 70.90% 26.90% 2.18% 0.00% NA
Indica II  465 51.80% 44.10% 4.09% 0.00% NA
Indica III  913 43.20% 55.20% 1.64% 0.00% NA
Indica Intermediate  786 53.80% 43.80% 2.42% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 96.20% 3.60% 0.20% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 50.00% 46.90% 3.12% 0.00% NA
Intermediate  90 80.00% 15.60% 4.44% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1124304377 C -> T LOC_Os11g40690.1 intron_variant ; MODIFIER silent_mutation Average:29.617; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124304377 NA 6.80E-06 mr1084_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
vg1124304377 NA 1.90E-06 mr1115_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
vg1124304377 NA 2.45E-06 mr1205_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
vg1124304377 NA 4.90E-06 mr1209_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
vg1124304377 3.66E-06 3.66E-06 mr1209_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
vg1124304377 NA 8.25E-08 mr1238_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
vg1124304377 NA 1.15E-06 mr1376_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
vg1124304377 NA 7.67E-07 mr1431_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
vg1124304377 NA 8.16E-07 mr1484_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
vg1124304377 NA 6.80E-06 mr1566_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
vg1124304377 NA 3.20E-10 mr1609_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
vg1124304377 NA 7.61E-06 mr1735_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
vg1124304377 NA 1.61E-08 mr1795_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
vg1124304377 NA 1.41E-06 mr1900_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
vg1124304377 NA 4.15E-08 mr1909_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
vg1124304377 NA 9.84E-06 mr1909_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