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Detailed information for vg0501807710:

Variant ID: vg0501807710 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 1807710
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTTGCATAGCCGCCGACGGTTGACGGAACTTCTAGAAAATAAAAAATGAATTCCAACGATAGTTATGTTCGATTTTTAGAATCACAATGACAATAAAGA[C/G]
TAGGCGGCGGACGGGCCGTAAAGGAGCATAGTGCCATTGTTTGACGAGACTTCTAAAAATTATAAAAAATAAAACTCAACAAGACAATTAACTCTAAAAA

Reverse complement sequence

TTTTTAGAGTTAATTGTCTTGTTGAGTTTTATTTTTTATAATTTTTAGAAGTCTCGTCAAACAATGGCACTATGCTCCTTTACGGCCCGTCCGCCGCCTA[G/C]
TCTTTATTGTCATTGTGATTCTAAAAATCGAACATAACTATCGTTGGAATTCATTTTTTATTTTCTAGAAGTTCCGTCAACCGTCGGCGGCTATGCAACT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.30%	8.90%	3.05%	36.80%	NA
All Indica	2759	72.70%	0.20%	1.09%	26.02%	NA
All Japonica	1512	17.50%	26.70%	6.35%	49.54%	NA
Aus	269	9.70%	0.00%	4.83%	85.50%	NA
Indica I	595	99.30%	0.30%	0.34%	0.00%	NA
Indica II	465	78.10%	0.20%	0.86%	20.86%	NA
Indica III	913	49.50%	0.20%	1.86%	48.41%	NA
Indica Intermediate	786	76.30%	0.00%	0.89%	22.77%	NA
Temperate Japonica	767	16.80%	47.70%	9.91%	25.55%	NA
Tropical Japonica	504	19.60%	2.60%	2.38%	75.40%	NA
Japonica Intermediate	241	14.90%	10.00%	3.32%	71.78%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	45.60%	12.20%	5.56%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0501807710	C -> DEL	N	N	silent_mutation	Average:16.859; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0501807710	C -> G	LOC_Os05g04020.1	intron_variant ; MODIFIER	silent_mutation	Average:16.859; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0501807710	NA	1.41E-14	Spikelet_length	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
vg0501807710	NA	2.98E-06	mr1354	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
vg0501807710	3.37E-06	NA	mr1486	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
vg0501807710	NA	7.73E-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
vg0501807710	NA	1.31E-06	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
vg0501807710	NA	5.11E-10	mr1011_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
vg0501807710	NA	3.43E-06	mr1011_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
vg0501807710	NA	6.54E-06	mr1359_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
vg0501807710	NA	2.31E-07	mr1359_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
vg0501807710	NA	2.13E-11	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
vg0501807710	NA	6.75E-07	mr1568_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
vg0501807710	NA	3.86E-06	mr1588_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
vg0501807710	NA	1.43E-07	mr1748_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
vg0501807710	NA	2.47E-06	mr1768_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
vg0501807710	NA	8.79E-06	mr1902_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