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Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0139710848:

Variant ID: vg0139710848 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 39710848
Reference Allele: GTGGAACCAAlternative Allele: ATGGAACCA,G
Primary Allele: GTGGAACCASecondary Allele: ATGGAACCA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGTTTTCCGGCGACCTTCGATCAGCAACGGACCTCGGCAAATCGGCTTCCACCAGTGCAACGTTGAAGAAACTCCAGGAGGATGGCGCTCTTCCTGGCC[GTGGAACCA/ATGGAACCA,G]
TGGAGAGTGAAGCAGGAGGTACTAATCCTCAGCCCATCTTGGGTCGCATGGTTGCGATCGAAGATTATGTTCTCTGCGGTTTTCTCCCTCCTCCTTCCGA

Reverse complement sequence

TCGGAAGGAGGAGGGAGAAAACCGCAGAGAACATAATCTTCGATCGCAACCATGCGACCCAAGATGGGCTGAGGATTAGTACCTCCTGCTTCACTCTCCA[TGGTTCCAC/TGGTTCCAT,C]
GGCCAGGAAGAGCGCCATCCTCCTGGAGTTTCTTCAACGTTGCACTGGTGGAAGCCGATTTGCCGAGGTCCGTTGCTGATCGAAGGTCGCCGGAAAACGA

Allele Frequencies:

Populations Population SizeFrequency of GTGGAACCA(primary allele) Frequency of ATGGAACCA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.90% 8.70% 0.49% 0.00% NA
All Indica  2759 97.40% 2.60% 0.00% 0.00% NA
All Japonica  1512 98.30% 0.20% 1.52% 0.00% NA
Aus  269 3.70% 96.30% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 5.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 95.40% 0.00% 4.56% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 31.20% 68.80% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 0.00% 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
vg0139710848 GTGGAACCA -> G LOC_Os01g68340.1 frameshift_variant&start_lost ; p.Met1fs; HIGH N Average:46.669; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N
vg0139710848 GTGGAACCA -> G LOC_Os01g68330.1 upstream_gene_variant ; 2446.0bp to feature; MODIFIER N Average:46.669; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N
vg0139710848 GTGGAACCA -> G LOC_Os01g68340.1 upstream_gene_variant ; 7.0bp to feature; MODIFIER N Average:46.669; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N
vg0139710848 GTGGAACCA -> G LOC_Os01g68350.1 downstream_gene_variant ; 2880.0bp to feature; MODIFIER N Average:46.669; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N
vg0139710848 GTGGAACCA -> ATGGAACCA LOC_Os01g68330.1 upstream_gene_variant ; 2445.0bp to feature; MODIFIER silent_mutation Average:46.669; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N
vg0139710848 GTGGAACCA -> ATGGAACCA LOC_Os01g68340.1 upstream_gene_variant ; 8.0bp to feature; MODIFIER silent_mutation Average:46.669; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N
vg0139710848 GTGGAACCA -> ATGGAACCA LOC_Os01g68350.1 downstream_gene_variant ; 2881.0bp to feature; MODIFIER silent_mutation Average:46.669; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N
vg0139710848 GTGGAACCA -> ATGGAACCA LOC_Os01g68330-LOC_Os01g68340 intergenic_region ; MODIFIER silent_mutation Average:46.669; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0139710848 NA 3.10E-06 mr1126 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
vg0139710848 NA 9.92E-15 mr1231 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
vg0139710848 NA 2.80E-08 mr1415 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
vg0139710848 NA 3.92E-14 mr1522 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
vg0139710848 NA 2.80E-08 mr1567 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
vg0139710848 NA 6.21E-09 mr1866 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
vg0139710848 1.79E-06 NA mr1113_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
vg0139710848 2.98E-07 NA mr1114_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
vg0139710848 1.51E-07 NA mr1117_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
vg0139710848 5.19E-06 NA 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
vg0139710848 2.11E-07 NA mr1119_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
vg0139710848 8.78E-06 NA mr1120_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
vg0139710848 7.55E-08 NA mr1123_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
vg0139710848 NA 9.24E-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
vg0139710848 2.53E-07 NA mr1240_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
vg0139710848 3.83E-08 NA 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
vg0139710848 2.09E-07 NA mr1247_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
vg0139710848 1.35E-07 NA 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
vg0139710848 NA 3.61E-06 mr1522_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
vg0139710848 NA 7.97E-08 mr1567_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