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Detailed information for vg0608860294:

Variant ID: vg0608860294 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 8860294
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCACAATGTCGAAGCCGAATTGCACAGCCGGCCGAAACACGTGCCAAAGCCCACCCCGCATGACAAAATAGTAAAAGTGCAGATTGACCATGCCGACCC[C/T]
GCAAAGCTCGTATCACTGGGGGACGGCATGGGTGAACAAGAAGCTGAGGGCATCCTAGCGGTGCTCAAAAAGAACATTGATATTTTCGCTTGGAGCCCCG

Reverse complement sequence

CGGGGCTCCAAGCGAAAATATCAATGTTCTTTTTGAGCACCGCTAGGATGCCCTCAGCTTCTTGTTCACCCATGCCGTCCCCCAGTGATACGAGCTTTGC[G/A]
GGGTCGGCATGGTCAATCTGCACTTTTACTATTTTGTCATGCGGGGTGGGCTTTGGCACGTGTTTCGGCCGGCTGTGCAATTCGGCTTCGACATTGTGCA

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 82.00% 3.70% 1.27% 13.03% NA
All Indica  2759 99.70% 0.00% 0.14% 0.14% NA
All Japonica  1512 47.30% 11.40% 2.98% 38.29% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.20% 0.00% 0.50% 0.34% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.00% 0.11% NA
Indica Intermediate  786 99.70% 0.00% 0.13% 0.13% NA
Temperate Japonica  767 77.20% 0.00% 1.04% 21.77% NA
Tropical Japonica  504 13.30% 31.00% 5.16% 50.60% NA
Japonica Intermediate  241 23.20% 7.10% 4.56% 65.15% NA
VI/Aromatic  96 61.50% 0.00% 10.42% 28.12% NA
Intermediate  90 91.10% 2.20% 0.00% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0608860294 C -> T LOC_Os06g15640.1 synonymous_variant ; p.Pro480Pro; LOW synonymous_codon Average:16.252; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0608860294 C -> DEL LOC_Os06g15640.1 N frameshift_variant Average:16.252; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0608860294 1.01E-06 9.29E-08 mr1215 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
vg0608860294 1.27E-07 9.04E-10 mr1218 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
vg0608860294 3.57E-06 3.57E-06 mr1256 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
vg0608860294 NA 4.69E-06 mr1304 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
vg0608860294 NA 6.24E-06 mr1350 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
vg0608860294 NA 2.52E-07 mr1401 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
vg0608860294 NA 3.34E-06 mr1414 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
vg0608860294 1.22E-06 2.09E-09 mr1422 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
vg0608860294 7.25E-06 4.42E-10 mr1583 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
vg0608860294 NA 3.04E-06 mr1638 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
vg0608860294 NA 4.70E-06 mr1072_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
vg0608860294 NA 6.60E-06 mr1075_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
vg0608860294 NA 1.24E-07 mr1077_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
vg0608860294 NA 2.98E-08 mr1136_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
vg0608860294 NA 1.12E-06 mr1222_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
vg0608860294 NA 1.35E-06 mr1850_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
vg0608860294 NA 1.26E-06 mr1929_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