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Detailed information for vg0403055424:

Variant ID: vg0403055424 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3055424
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGATTGCCCAAGACATCAACAGGATATGATTCCATTTGGGTGATCGTGGATCGCCTCACCAAGACGGCGAGATTCATTCCCGTTAAGACAAATTATAG[C/T]
AGTGCTAAGCTAGCCGAGTTATACATGACCAGGATAGTATGTCTTCATGGATGTACCTAAGATAATTATATCTGATCGAGGCACACAGTTTACCTCGCAT

Reverse complement sequence

ATGCGAGGTAAACTGTGTGCCTCGATCAGATATAATTATCTTAGGTACATCCATGAAGACATACTATCCTGGTCATGTATAACTCGGCTAGCTTAGCACT[G/A]
CTATAATTTGTCTTAACGGGAATGAATCTCGCCGTCTTGGTGAGGCGATCCACGATCACCCAAATGGAATCATATCCTGTTGATGTCTTGGGCAATCCAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.70%	3.40%	18.15%	17.75%	NA
All Indica	2759	60.10%	0.10%	17.80%	22.00%	NA
All Japonica	1512	54.40%	10.40%	22.09%	13.03%	NA
Aus	269	92.90%	0.00%	3.35%	3.72%	NA
Indica I	595	30.10%	0.00%	9.08%	60.84%	NA
Indica II	465	81.50%	0.40%	11.61%	6.45%	NA
Indica III	913	63.70%	0.00%	27.16%	9.09%	NA
Indica Intermediate	786	65.90%	0.10%	17.18%	16.79%	NA
Temperate Japonica	767	73.50%	1.70%	11.21%	13.56%	NA
Tropical Japonica	504	36.10%	23.60%	32.74%	7.54%	NA
Japonica Intermediate	241	32.00%	10.80%	34.44%	22.82%	NA
VI/Aromatic	96	77.10%	0.00%	10.42%	12.50%	NA
Intermediate	90	70.00%	0.00%	15.56%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403055424	C -> DEL	LOC_Os04g05900.1	N	frameshift_variant	Average:9.027; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0403055424	C -> T	LOC_Os04g05900.1	synonymous_variant ; p.Ser958Ser; LOW	synonymous_codon	Average:9.027; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403055424	3.09E-15	1.85E-31	mr1301	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
vg0403055424	4.16E-07	7.24E-20	mr1301	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
vg0403055424	4.79E-15	1.48E-27	mr1410	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
vg0403055424	2.47E-06	9.12E-18	mr1410	Jap_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
vg0403055424	NA	1.59E-31	mr1699	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
vg0403055424	NA	5.20E-08	mr1993	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
vg0403055424	NA	6.26E-09	mr1993	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
vg0403055424	6.21E-14	1.96E-31	mr1301_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
vg0403055424	4.63E-06	2.26E-20	mr1301_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
vg0403055424	1.65E-11	1.44E-25	mr1410_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
vg0403055424	NA	2.65E-16	mr1410_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
vg0403055424	NA	8.11E-29	mr1699_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
vg0403055424	NA	2.37E-09	mr1769_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
vg0403055424	7.35E-06	NA	mr1798_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
vg0403055424	2.36E-08	6.57E-15	mr1993_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
vg0403055424	2.48E-06	1.33E-13	mr1993_2	Jap_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