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Detailed information for vg1007671817:

Variant ID: vg1007671817 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 7671817
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCGCTGAATAGCCCGATGGAACTTTAATATCCTTCAAGCATGATAACATTGCGATCTTCTCATCCTTCGACAGTGTGTGGCAGGCTGGAGGGACGTACA[C/T]
TTTACTTGTCTCTGCATCTCGTATGGGCTGGAGTTCGCTGCGAATATTCATGTCCTGTAGATCAAGGCGCGCGTTCAACCCGTCCTTTGTCTTCCCGGGA

Reverse complement sequence

TCCCGGGAAGACAAAGGACGGGTTGAACGCGCGCCTTGATCTACAGGACATGAATATTCGCAGCGAACTCCAGCCCATACGAGATGCAGAGACAAGTAAA[G/A]
TGTACGTCCCTCCAGCCTGCCACACACTGTCGAAGGATGAGAAGATCGCAATGTTATCATGCTTGAAGGATATTAAAGTTCCATCGGGCTATTCAGCGAG

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 14.40% 0.10% 11.70% 73.78% NA
All Indica  2759 2.00% 0.30% 5.98% 91.77% NA
All Japonica  1512 39.60% 0.00% 8.40% 51.98% NA
Aus  269 2.20% 0.00% 73.61% 24.16% NA
Indica I  595 1.00% 0.20% 0.50% 98.32% NA
Indica II  465 1.90% 0.00% 4.95% 93.12% NA
Indica III  913 2.30% 0.70% 8.21% 88.83% NA
Indica Intermediate  786 2.40% 0.00% 8.14% 89.44% NA
Temperate Japonica  767 53.70% 0.00% 3.13% 43.16% NA
Tropical Japonica  504 10.70% 0.00% 13.89% 75.40% NA
Japonica Intermediate  241 55.20% 0.00% 13.69% 31.12% NA
VI/Aromatic  96 1.00% 0.00% 50.00% 48.96% NA
Intermediate  90 20.00% 0.00% 16.67% 63.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1007671817 C -> T LOC_Os10g14130.1 missense_variant ; p.Val142Met; MODERATE nonsynonymous_codon ; V142M Average:6.753; most accessible tissue: Minghui63 panicle, score: 16.27 probably damaging 2.247 TOLERATED 0.07
vg1007671817 C -> DEL LOC_Os10g14130.1 N frameshift_variant Average:6.753; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1007671817 NA 1.19E-06 Spikelet_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1007671817 NA 1.17E-38 mr1026 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
vg1007671817 NA 4.51E-13 mr1026 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
vg1007671817 NA 2.62E-07 mr1113 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
vg1007671817 NA 5.46E-07 mr1114 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
vg1007671817 1.23E-07 8.81E-09 mr1116 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
vg1007671817 NA 2.50E-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
vg1007671817 5.74E-06 8.93E-19 mr1118 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
vg1007671817 NA 3.55E-06 mr1120 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
vg1007671817 NA 3.29E-36 mr1161 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
vg1007671817 NA 1.44E-11 mr1161 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
vg1007671817 2.69E-06 4.49E-08 mr1247 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
vg1007671817 NA 6.07E-06 mr1261 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
vg1007671817 NA 6.31E-18 mr1495 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
vg1007671817 NA 5.86E-06 mr1496 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
vg1007671817 6.85E-07 7.67E-10 mr1794 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
vg1007671817 NA 8.26E-06 mr1113_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
vg1007671817 NA 7.58E-06 mr1114_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
vg1007671817 NA 1.00E-18 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
vg1007671817 6.68E-08 2.45E-23 mr1118_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
vg1007671817 NA 8.16E-08 mr1120_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
vg1007671817 NA 7.32E-06 mr1123_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
vg1007671817 NA 1.39E-40 mr1161_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
vg1007671817 NA 2.69E-14 mr1161_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
vg1007671817 NA 2.99E-07 mr1247_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
vg1007671817 9.64E-07 2.92E-26 mr1495_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
vg1007671817 8.85E-09 1.67E-23 mr1495_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
vg1007671817 NA 1.03E-07 mr1496_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
vg1007671817 NA 2.14E-07 mr1936_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