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Detailed information for vg1000297002:

Variant ID: vg1000297002 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 297002
Reference Allele: ACCTAlternative Allele: CCCT,A
Primary Allele: ACCTSecondary Allele: CCCT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCCGAGCCGAACCACCGAACCATTGGCTTTTTATTAACACACCCTGTAACCAAGTCGAGCCGAACCACCAAACCATCGGCTTTTTAATTAATAACACAC[ACCT/CCCT,A]
CCCCCTCTCTCTCCCTTATCCTCTCCTACTCTTAGTCTCTCCACTCATGCCCAACGCTTCCTATCCTCTCCCTCTTCCCTGCAGGCGGAGCTAGAATGAA

Reverse complement sequence

TTCATTCTAGCTCCGCCTGCAGGGAAGAGGGAGAGGATAGGAAGCGTTGGGCATGAGTGGAGAGACTAAGAGTAGGAGAGGATAAGGGAGAGAGAGGGGG[AGGT/AGGG,T]
GTGTGTTATTAATTAAAAAGCCGATGGTTTGGTGGTTCGGCTCGACTTGGTTACAGGGTGTGTTAATAAAAAGCCAATGGTTCGGTGGTTCGGCTCGGCT

Allele Frequencies:

Populations Population SizeFrequency of ACCT(primary allele) Frequency of CCCT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.50% 30.20% 3.17% 0.04% A: 0.04%
All Indica  2759 63.20% 33.00% 3.62% 0.07% A: 0.07%
All Japonica  1512 65.10% 31.90% 2.91% 0.00% NA
Aus  269 95.90% 2.20% 1.86% 0.00% NA
Indica I  595 61.30% 34.80% 3.70% 0.17% NA
Indica II  465 65.40% 28.80% 5.81% 0.00% NA
Indica III  913 55.10% 41.40% 3.40% 0.11% NA
Indica Intermediate  786 72.80% 24.40% 2.54% 0.00% A: 0.25%
Temperate Japonica  767 88.70% 10.80% 0.52% 0.00% NA
Tropical Japonica  504 29.60% 63.30% 7.14% 0.00% NA
Japonica Intermediate  241 64.70% 33.60% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 66.70% 32.20% 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
vg1000297002 ACCT -> CCCT LOC_Os10g01480.1 downstream_gene_variant ; 4769.0bp to feature; MODIFIER silent_mutation Average:81.101; most accessible tissue: Minghui63 root, score: 97.511 N N N N
vg1000297002 ACCT -> CCCT LOC_Os10g01470-LOC_Os10g01480 intergenic_region ; MODIFIER silent_mutation Average:81.101; most accessible tissue: Minghui63 root, score: 97.511 N N N N
vg1000297002 ACCT -> A LOC_Os10g01480.1 downstream_gene_variant ; 4768.0bp to feature; MODIFIER silent_mutation Average:81.101; most accessible tissue: Minghui63 root, score: 97.511 N N N N
vg1000297002 ACCT -> A LOC_Os10g01470-LOC_Os10g01480 intergenic_region ; MODIFIER silent_mutation Average:81.101; most accessible tissue: Minghui63 root, score: 97.511 N N N N
vg1000297002 ACCT -> DEL N N silent_mutation Average:81.101; most accessible tissue: Minghui63 root, score: 97.511 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)
vg1000297002 ACCT A 0.0 -0.21 0.02 0.04 0.03 0.04
vg1000297002 ACCT CCCT -0.14 -0.07 -0.01 0.03 -0.04 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000297002 2.61E-06 2.61E-06 mr1011 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
vg1000297002 NA 3.65E-06 mr1060 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
vg1000297002 NA 2.15E-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
vg1000297002 NA 7.85E-09 mr1156 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
vg1000297002 NA 8.40E-07 mr1163 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
vg1000297002 NA 1.06E-07 mr1179 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
vg1000297002 NA 8.21E-07 mr1192 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
vg1000297002 NA 1.68E-08 mr1300 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
vg1000297002 NA 2.86E-10 mr1310 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
vg1000297002 8.50E-08 NA mr1486 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
vg1000297002 NA 1.27E-06 mr1486 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
vg1000297002 NA 4.29E-11 mr1486 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
vg1000297002 NA 3.63E-07 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
vg1000297002 NA 2.08E-06 mr1520 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
vg1000297002 NA 8.24E-12 mr1539 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
vg1000297002 NA 1.32E-10 mr1539 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
vg1000297002 NA 1.29E-14 mr1540 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
vg1000297002 NA 3.79E-07 mr1548 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
vg1000297002 NA 8.09E-12 mr1549 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
vg1000297002 NA 2.44E-07 mr1570 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
vg1000297002 NA 1.58E-10 mr1580 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
vg1000297002 NA 8.77E-06 mr1588 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
vg1000297002 NA 4.64E-09 mr1624 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
vg1000297002 NA 1.75E-10 mr1624 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
vg1000297002 NA 1.83E-06 mr1729 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
vg1000297002 NA 3.80E-15 mr1732 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
vg1000297002 NA 1.20E-07 mr1733 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
vg1000297002 1.94E-06 1.01E-09 mr1736 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
vg1000297002 NA 1.00E-10 mr1757 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
vg1000297002 NA 9.75E-06 mr1780 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
vg1000297002 NA 6.93E-10 mr1825 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
vg1000297002 NA 1.44E-06 mr1912 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
vg1000297002 NA 5.67E-10 mr1926 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
vg1000297002 NA 1.53E-07 mr1126_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
vg1000297002 NA 8.50E-08 mr1156_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
vg1000297002 NA 9.11E-12 mr1310_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
vg1000297002 NA 4.77E-09 mr1364_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
vg1000297002 9.02E-09 NA mr1486_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
vg1000297002 NA 3.54E-06 mr1486_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
vg1000297002 NA 8.96E-10 mr1486_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
vg1000297002 NA 2.86E-06 mr1721_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
vg1000297002 NA 1.47E-08 mr1959_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