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Detailed information for vg1006587700:

Variant ID: vg1006587700 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 6587700
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAATGTACCGGACCAGCTATTCTTGCTTGAGCAGGTAGATGGACCATCAAGTGTATCATAATAGTAAAAAATGAGGGTAGGAATATTTTCTCAAGAAGA[C/A]
ATATGGTCTCAGCTATTTCTGCCTCTAGTTTTTGCATATCACTTACACGGATAACAGGCGAATATATTTGCTTAAAAAAATTGCTCACACGAATCAGTGC

Reverse complement sequence

GCACTGATTCGTGTGAGCAATTTTTTTAAGCAAATATATTCGCCTGTTATCCGTGTAAGTGATATGCAAAAACTAGAGGCAGAAATAGCTGAGACCATAT[G/T]
TCTTCTTGAGAAAATATTCCTACCCTCATTTTTTACTATTATGATACACTTGATGGTCCATCTACCTGCTCAAGCAAGAATAGCTGGTCCGGTACATTTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.60% 2.60% 2.62% 15.11% NA
All Indica  2759 78.40% 0.20% 3.84% 17.58% NA
All Japonica  1512 76.90% 7.90% 0.73% 14.48% NA
Aus  269 97.40% 0.00% 2.23% 0.37% NA
Indica I  595 86.20% 0.00% 2.86% 10.92% NA
Indica II  465 86.00% 0.20% 3.44% 10.32% NA
Indica III  913 69.40% 0.20% 4.27% 26.07% NA
Indica Intermediate  786 78.40% 0.30% 4.33% 17.05% NA
Temperate Japonica  767 84.70% 0.30% 0.52% 14.47% NA
Tropical Japonica  504 65.30% 21.40% 0.79% 12.50% NA
Japonica Intermediate  241 75.90% 4.10% 1.24% 18.67% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 90.00% 0.00% 1.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1006587700 C -> A LOC_Os10g11870.1 missense_variant ; p.Cys712Phe; MODERATE nonsynonymous_codon ; C712F Average:14.468; most accessible tissue: Zhenshan97 panicle, score: 28.447 probably damaging 2.392 DELETERIOUS 0.00
vg1006587700 C -> DEL LOC_Os10g11870.1 N frameshift_variant Average:14.468; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1006587700 1.91E-09 5.39E-14 mr1016 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
vg1006587700 1.24E-09 1.11E-13 mr1017 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
vg1006587700 2.23E-07 5.54E-11 mr1018 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
vg1006587700 3.29E-08 1.32E-12 mr1019 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
vg1006587700 4.78E-09 7.86E-14 mr1055 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
vg1006587700 9.76E-09 4.05E-13 mr1132 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
vg1006587700 3.77E-06 1.60E-10 mr1178 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
vg1006587700 NA 5.77E-06 mr1364 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
vg1006587700 1.87E-07 2.19E-11 mr1390 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
vg1006587700 NA 1.35E-06 mr1443 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
vg1006587700 7.22E-07 3.77E-11 mr1490 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
vg1006587700 1.78E-07 NA mr1023_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
vg1006587700 1.21E-10 1.18E-13 mr1055_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
vg1006587700 5.14E-06 NA mr1079_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
vg1006587700 9.98E-13 1.86E-15 mr1132_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
vg1006587700 6.31E-07 NA mr1178_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
vg1006587700 4.64E-06 7.10E-09 mr1261_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
vg1006587700 1.89E-10 1.27E-13 mr1390_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
vg1006587700 3.12E-07 NA mr1489_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
vg1006587700 5.74E-12 1.21E-14 mr1490_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