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Detailed information for vg0304001174:

Variant ID: vg0304001174 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 4001174
Reference Allele: GAlternative Allele: A,GTAAATTTA
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.11, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


CAAAAAATAGTCGGCAAGTATTTACATTATAAGTCCCTAAATTTCATATGTAATTTTAGTGTATTTACAATGTAAGTCTTAGAATTACATATGTAAATTT[G/A,GTAAATTTA]
AAAATTACATACTAATTACATATGTAAGTGGGGTGTAAATGAGGTGTAACTACTGTGTAAGTGGCTAAAAAAAAATCGACTGTAGCATATAGCGCCATAT

Reverse complement sequence

ATATGGCGCTATATGCTACAGTCGATTTTTTTTTAGCCACTTACACAGTAGTTACACCTCATTTACACCCCACTTACATATGTAATTAGTATGTAATTTT[C/T,TAAATTTAC]
AAATTTACATATGTAATTCTAAGACTTACATTGTAAATACACTAAAATTACATATGAAATTTAGGGACTTATAATGTAAATACTTGCCGACTATTTTTTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.80% 32.40% 0.59% 0.00% GTAAATTTA: 6.22%
All Indica  2759 95.30% 2.10% 0.14% 0.00% GTAAATTTA: 2.46%
All Japonica  1512 9.80% 89.10% 1.06% 0.00% GTAAATTTA: 0.07%
Aus  269 22.30% 0.40% 1.49% 0.00% GTAAATTTA: 75.84%
Indica I  595 97.30% 2.40% 0.17% 0.00% GTAAATTTA: 0.17%
Indica II  465 92.90% 4.70% 0.43% 0.00% GTAAATTTA: 1.94%
Indica III  913 95.90% 0.30% 0.00% 0.00% GTAAATTTA: 3.72%
Indica Intermediate  786 94.30% 2.50% 0.13% 0.00% GTAAATTTA: 3.05%
Temperate Japonica  767 2.60% 96.10% 1.30% 0.00% NA
Tropical Japonica  504 6.30% 93.50% 0.20% 0.00% NA
Japonica Intermediate  241 39.80% 57.70% 2.07% 0.00% GTAAATTTA: 0.41%
VI/Aromatic  96 3.10% 82.30% 0.00% 0.00% GTAAATTTA: 14.58%
Intermediate  90 38.90% 48.90% 4.44% 0.00% GTAAATTTA: 7.78%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0304001174 G -> A LOC_Os03g07870.1 upstream_gene_variant ; 1142.0bp to feature; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N
vg0304001174 G -> A LOC_Os03g07850.1 downstream_gene_variant ; 3359.0bp to feature; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N
vg0304001174 G -> A LOC_Os03g07880.1 downstream_gene_variant ; 821.0bp to feature; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N
vg0304001174 G -> A LOC_Os03g07880.2 downstream_gene_variant ; 821.0bp to feature; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N
vg0304001174 G -> A LOC_Os03g07880.3 downstream_gene_variant ; 821.0bp to feature; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N
vg0304001174 G -> A LOC_Os03g07870-LOC_Os03g07880 intergenic_region ; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N
vg0304001174 G -> GTAAATTTA LOC_Os03g07870.1 upstream_gene_variant ; 1143.0bp to feature; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N
vg0304001174 G -> GTAAATTTA LOC_Os03g07850.1 downstream_gene_variant ; 3360.0bp to feature; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N
vg0304001174 G -> GTAAATTTA LOC_Os03g07880.1 downstream_gene_variant ; 820.0bp to feature; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N
vg0304001174 G -> GTAAATTTA LOC_Os03g07880.2 downstream_gene_variant ; 820.0bp to feature; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N
vg0304001174 G -> GTAAATTTA LOC_Os03g07880.3 downstream_gene_variant ; 820.0bp to feature; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N
vg0304001174 G -> GTAAATTTA LOC_Os03g07870-LOC_Os03g07880 intergenic_region ; MODIFIER silent_mutation Average:94.665; most accessible tissue: Minghui63 flower, score: 99.242 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0304001174 G A 0.01 -0.01 -0.02 0.0 -0.01 0.01
vg0304001174 G GTAAA* -0.03 -0.01 -0.02 -0.07 -0.04 -0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0304001174 NA 5.40E-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
vg0304001174 NA 2.22E-15 mr1118 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
vg0304001174 NA 7.74E-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
vg0304001174 NA 2.11E-14 mr1146 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
vg0304001174 NA 1.62E-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
vg0304001174 NA 3.36E-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
vg0304001174 NA 4.30E-13 mr1239 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
vg0304001174 NA 1.98E-20 mr1242 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
vg0304001174 NA 5.48E-12 mr1902 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
vg0304001174 NA 9.41E-24 mr1917 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
vg0304001174 NA 4.89E-20 mr1010_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
vg0304001174 NA 1.30E-13 mr1035_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
vg0304001174 NA 6.61E-07 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
vg0304001174 NA 4.53E-15 mr1118_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
vg0304001174 NA 2.31E-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
vg0304001174 NA 3.29E-06 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
vg0304001174 NA 1.83E-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
vg0304001174 NA 8.49E-28 mr1149_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
vg0304001174 NA 3.77E-06 mr1149_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
vg0304001174 NA 8.41E-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
vg0304001174 1.59E-07 1.59E-07 mr1197_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
vg0304001174 NA 1.82E-06 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
vg0304001174 NA 1.34E-23 mr1242_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
vg0304001174 NA 1.72E-17 mr1281_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
vg0304001174 NA 2.95E-10 mr1299_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
vg0304001174 NA 2.35E-09 mr1398_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
vg0304001174 NA 1.73E-26 mr1441_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
vg0304001174 NA 9.58E-06 mr1441_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
vg0304001174 NA 6.07E-47 mr1486_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
vg0304001174 NA 2.75E-15 mr1496_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
vg0304001174 NA 7.58E-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
vg0304001174 NA 1.01E-11 mr1537_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
vg0304001174 NA 3.00E-17 mr1592_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
vg0304001174 NA 3.60E-13 mr1595_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
vg0304001174 NA 9.94E-10 mr1600_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
vg0304001174 NA 2.11E-37 mr1689_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
vg0304001174 NA 1.88E-09 mr1700_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
vg0304001174 NA 5.18E-23 mr1708_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
vg0304001174 NA 3.55E-14 mr1713_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
vg0304001174 NA 2.49E-08 mr1727_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
vg0304001174 NA 2.48E-11 mr1756_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
vg0304001174 NA 1.77E-08 mr1783_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
vg0304001174 NA 3.43E-06 mr1785_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
vg0304001174 NA 6.70E-09 mr1804_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
vg0304001174 NA 2.68E-06 mr1840_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
vg0304001174 NA 1.15E-15 mr1842_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
vg0304001174 NA 5.38E-48 mr1861_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