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Detailed information for vg0906459575:

Variant ID: vg0906459575 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6459575
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGGGATAGCTTATGCCGATCCCGTGTAGTTTGAATTTTCCTCAAAACCAGGTCGCCGACTAAGAAAGCTCGCGATCGGACGTTACGATTATGATAATGA[T/C]
GCAAACCTTGCAGGTATCGGGCCGACTGAATTAAGGCTGCTTCACGGGCCTCTTCCAGTCGGTGTAGGTCATCCACTCGGTCGTCTCCGTAGCGCTCTTC

Reverse complement sequence

GAAGAGCGCTACGGAGACGACCGAGTGGATGACCTACACCGACTGGAAGAGGCCCGTGAAGCAGCCTTAATTCAGTCGGCCCGATACCTGCAAGGTTTGC[A/G]
TCATTATCATAATCGTAACGTCCGATCGCGAGCTTTCTTAGTCGGCGACCTGGTTTTGAGGAAAATTCAAACTACACGGGATCGGCATAAGCTATCCCCT

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 69.70% 12.10% 1.14% 17.08% NA
All Indica  2759 68.80% 4.00% 1.38% 25.92% NA
All Japonica  1512 84.70% 14.90% 0.00% 0.33% NA
Aus  269 11.20% 68.80% 2.23% 17.84% NA
Indica I  595 96.50% 1.00% 0.17% 2.35% NA
Indica II  465 50.30% 7.10% 3.01% 39.57% NA
Indica III  913 63.50% 1.80% 0.77% 33.95% NA
Indica Intermediate  786 64.80% 6.90% 2.04% 26.34% NA
Temperate Japonica  767 95.40% 4.30% 0.00% 0.26% NA
Tropical Japonica  504 86.10% 13.70% 0.00% 0.20% NA
Japonica Intermediate  241 47.70% 51.50% 0.00% 0.83% NA
VI/Aromatic  96 19.80% 42.70% 9.38% 28.12% NA
Intermediate  90 73.30% 12.20% 1.11% 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
vg0906459575 T -> DEL LOC_Os09g11580.1 N frameshift_variant Average:41.204; most accessible tissue: Minghui63 young leaf, score: 62.741 N N N N
vg0906459575 T -> C LOC_Os09g11580.1 missense_variant ; p.His1513Arg; MODERATE nonsynonymous_codon ; H1513R Average:41.204; most accessible tissue: Minghui63 young leaf, score: 62.741 benign -0.677 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906459575 NA 7.86E-06 mr1114 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
vg0906459575 NA 3.71E-06 mr1117 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
vg0906459575 NA 2.21E-06 mr1118 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
vg0906459575 NA 3.06E-06 mr1123 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
vg0906459575 NA 4.93E-07 mr1180 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
vg0906459575 NA 2.40E-06 mr1183 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
vg0906459575 NA 6.55E-06 mr1242 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
vg0906459575 NA 9.15E-06 mr1496 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
vg0906459575 NA 3.27E-09 mr1498 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
vg0906459575 NA 3.25E-06 mr1503 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
vg0906459575 NA 9.37E-06 mr1113_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
vg0906459575 NA 5.51E-07 mr1114_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
vg0906459575 NA 4.70E-08 mr1117_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
vg0906459575 NA 5.17E-06 mr1118_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
vg0906459575 NA 3.76E-07 mr1119_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
vg0906459575 NA 1.15E-06 mr1120_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
vg0906459575 NA 1.07E-06 mr1123_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
vg0906459575 NA 5.62E-07 mr1180_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
vg0906459575 NA 1.05E-07 mr1183_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
vg0906459575 NA 2.41E-08 mr1240_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
vg0906459575 NA 1.65E-06 mr1242_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
vg0906459575 NA 3.26E-06 mr1247_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
vg0906459575 NA 9.22E-09 mr1310_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
vg0906459575 NA 1.74E-08 mr1496_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
vg0906459575 NA 1.56E-09 mr1498_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
vg0906459575 NA 9.14E-08 mr1679_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
vg0906459575 NA 2.59E-06 mr1691_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
vg0906459575 NA 1.58E-10 mr1769_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
vg0906459575 NA 3.83E-08 mr1794_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
vg0906459575 NA 2.88E-06 mr1925_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
vg0906459575 NA 3.64E-08 mr1951_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
vg0906459575 NA 5.60E-15 mr1961_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