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Detailed information for vg1002009944:

Variant ID: vg1002009944 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2009944
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATACATGAGGTAGGCAGCCTAAAGCCACGAACCAAACTTATACTAGGAGTCCTAAACACCTTAGGAAACCCTCTAGTACAAGAAAGAAACTTTACATAAC[C/T]
AGTCGTACCAAATTTGGACTCCTTCCAAATTCGACTCCGCATCCCATACGCACACAATAACTCCATCGTATGCCATATGGAATCTCCATCAACCACGTGC

Reverse complement sequence

GCACGTGGTTGATGGAGATTCCATATGGCATACGATGGAGTTATTGTGTGCGTATGGGATGCGGAGTCGAATTTGGAAGGAGTCCAAATTTGGTACGACT[G/A]
GTTATGTAAAGTTTCTTTCTTGTACTAGAGGGTTTCCTAAGGTGTTTAGGACTCCTAGTATAAGTTTGGTTCGTGGCTTTAGGCTGCCTACCTCATGTAT

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 95.80% 1.90% 1.38% 0.97% NA
All Indica  2759 96.40% 0.20% 1.78% 1.63% NA
All Japonica  1512 94.80% 4.90% 0.26% 0.00% NA
Aus  269 94.80% 0.70% 4.09% 0.37% NA
Indica I  595 96.10% 0.20% 2.86% 0.84% NA
Indica II  465 98.10% 0.20% 0.65% 1.08% NA
Indica III  913 95.70% 0.20% 1.86% 2.19% NA
Indica Intermediate  786 96.40% 0.10% 1.53% 1.91% NA
Temperate Japonica  767 98.20% 1.30% 0.52% 0.00% NA
Tropical Japonica  504 96.00% 4.00% 0.00% 0.00% NA
Japonica Intermediate  241 81.70% 18.30% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 95.60% 3.30% 1.11% 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
vg1002009944 C -> T LOC_Os10g04280.1 upstream_gene_variant ; 1055.0bp to feature; MODIFIER silent_mutation Average:31.283; most accessible tissue: Minghui63 flag leaf, score: 56.489 N N N N
vg1002009944 C -> T LOC_Os10g04270-LOC_Os10g04280 intergenic_region ; MODIFIER silent_mutation Average:31.283; most accessible tissue: Minghui63 flag leaf, score: 56.489 N N N N
vg1002009944 C -> DEL N N silent_mutation Average:31.283; most accessible tissue: Minghui63 flag leaf, score: 56.489 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002009944 NA 9.75E-06 mr1113 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
vg1002009944 7.83E-07 1.55E-08 mr1114 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
vg1002009944 NA 6.23E-06 mr1116 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
vg1002009944 4.02E-06 1.64E-08 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
vg1002009944 1.94E-06 1.04E-09 mr1118 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
vg1002009944 3.19E-06 1.71E-07 mr1119 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
vg1002009944 4.79E-06 2.80E-07 mr1120 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
vg1002009944 2.33E-06 6.35E-09 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
vg1002009944 NA 8.23E-06 mr1240 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
vg1002009944 1.37E-07 1.88E-10 mr1242 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
vg1002009944 2.01E-06 5.22E-08 mr1247 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
vg1002009944 NA 1.26E-06 mr1495 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
vg1002009944 7.70E-06 4.28E-08 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
vg1002009944 NA 8.43E-07 mr1917 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
vg1002009944 NA 2.33E-07 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
vg1002009944 1.13E-07 2.04E-09 mr1114_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
vg1002009944 2.13E-07 1.63E-09 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
vg1002009944 NA 9.39E-09 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
vg1002009944 1.47E-06 1.24E-08 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
vg1002009944 4.58E-07 8.89E-09 mr1120_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
vg1002009944 4.03E-07 1.64E-09 mr1123_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
vg1002009944 3.26E-08 5.96E-11 mr1240_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
vg1002009944 3.93E-06 7.88E-09 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
vg1002009944 1.74E-06 3.69E-08 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
vg1002009944 1.37E-06 9.61E-10 mr1495_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
vg1002009944 4.76E-08 4.47E-11 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
vg1002009944 1.99E-06 3.35E-08 mr1936_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