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Detailed information for vg0610630630:

Variant ID: vg0610630630 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 10630630
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCTGGCAATAATTCCGGTACTCGAGTTTGAACCGCACGCATCGCATAACGTCGAGGACCAAACTCTTGACGCGGAGGTCGAAGTGACAGCAACTGGCCC[G/A]
AGTGAGTGATCCTGTCAACCTTGATGCTGTTTTGGGGGTTTCCGAGTTATCTTAGTAGTCGTTATGTTTAGCAGATCTCGAGGATTCCCTTGCGACCCAA

Reverse complement sequence

TTGGGTCGCAAGGGAATCCTCGAGATCTGCTAAACATAACGACTACTAAGATAACTCGGAAACCCCCAAAACAGCATCAAGGTTGACAGGATCACTCACT[C/T]
GGGCCAGTTGCTGTCACTTCGACCTCCGCGTCAAGAGTTTGGTCCTCGACGTTATGCGATGCGTGCGGTTCAAACTCGAGTACCGGAATTATTGCCAGCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.30% 1.20% 11.28% 28.27% NA
All Indica  2759 41.70% 2.00% 18.63% 37.69% NA
All Japonica  1512 82.90% 0.00% 0.40% 16.67% NA
Aus  269 98.10% 0.00% 0.37% 1.49% NA
Indica I  595 31.30% 0.70% 10.76% 57.31% NA
Indica II  465 17.20% 1.90% 19.78% 61.08% NA
Indica III  913 57.20% 2.30% 23.88% 16.65% NA
Indica Intermediate  786 46.10% 2.70% 17.81% 33.46% NA
Temperate Japonica  767 88.00% 0.00% 0.39% 11.60% NA
Tropical Japonica  504 72.20% 0.00% 0.40% 27.38% NA
Japonica Intermediate  241 89.20% 0.00% 0.41% 10.37% NA
VI/Aromatic  96 90.60% 0.00% 0.00% 9.38% NA
Intermediate  90 52.20% 0.00% 13.33% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0610630630 G -> A LOC_Os06g18750.1 splice_region_variant&synonymous_variant ; p.Pro119Pro; LOW synonymous_codon Average:14.259; most accessible tissue: Callus, score: 34.575 N N N N
vg0610630630 G -> DEL LOC_Os06g18750.1 N frameshift_variant Average:14.259; most accessible tissue: Callus, score: 34.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0610630630 9.69E-07 NA mr1090 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
vg0610630630 5.25E-06 NA mr1094 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
vg0610630630 6.66E-06 NA mr1111 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
vg0610630630 6.98E-06 NA mr1090_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
vg0610630630 NA 4.50E-07 mr1090_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
vg0610630630 5.02E-07 NA mr1094_2 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
vg0610630630 NA 3.33E-06 mr1094_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
vg0610630630 5.37E-07 NA mr1111_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
vg0610630630 6.03E-06 NA mr1111_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
vg0610630630 6.33E-07 NA mr1144_2 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