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Detailed information for vg0315675411:

Variant ID: vg0315675411 (JBrowse)	Variation Type: INDEL
Chromosome: chr03	Position: 15675411
Reference Allele: A	Alternative Allele: T,AT
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAATAAATTTGTCTCGCAGTTTACATGCGGAATTTGTAATTTGTTTTATTATTAGTCTATATTTAGTTCTTCAAATGTGTGTCCGTATACTTAAAAAAAA[A/T,AT]
TTGACTGTGGAATTAAACACGGCCTACGTATTTGAGAAAACATTGATGGTCAGAATTTTAAAAGCATGACTGAATTATATCCTGAATGTCAAATATTTTT

Reverse complement sequence

AAAAATATTTGACATTCAGGATATAATTCAGTCATGCTTTTAAAATTCTGACCATCAATGTTTTCTCAAATACGTAGGCCGTGTTTAATTCCACAGTCAA[T/A,AT]
TTTTTTTTAAGTATACGGACACACATTTGAAGAACTAAATATAGACTAATAATAAAACAAATTACAAATTCCGCATGTAAACTGCGAGACAAATTTATTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.10%	26.20%	0.02%	0.00%	AT: 0.66%
All Indica	2759	96.00%	3.20%	0.00%	0.00%	AT: 0.80%
All Japonica	1512	32.70%	66.70%	0.07%	0.00%	AT: 0.53%
Aus	269	81.80%	18.20%	0.00%	0.00%	NA
Indica I	595	99.00%	0.30%	0.00%	0.00%	AT: 0.67%
Indica II	465	98.10%	0.90%	0.00%	0.00%	AT: 1.08%
Indica III	913	95.10%	3.90%	0.00%	0.00%	AT: 0.99%
Indica Intermediate	786	93.80%	5.70%	0.00%	0.00%	AT: 0.51%
Temperate Japonica	767	4.30%	95.70%	0.00%	0.00%	NA
Tropical Japonica	504	77.20%	21.00%	0.20%	0.00%	AT: 1.59%
Japonica Intermediate	241	29.90%	70.10%	0.00%	0.00%	NA
VI/Aromatic	96	24.00%	76.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	23.30%	0.00%	0.00%	AT: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0315675411	A -> T	LOC_Os03g27370.1	intron_variant ; MODIFIER	silent_mutation	Average:37.631; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0315675411	A -> AT	LOC_Os03g27370.1	intron_variant ; MODIFIER	silent_mutation	Average:37.631; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315675411	NA	7.49E-14	Grain_length	Jap_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
vg0315675411	NA	1.57E-09	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
vg0315675411	NA	9.49E-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
vg0315675411	NA	4.51E-10	mr1679	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
vg0315675411	NA	1.94E-06	mr1693	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
vg0315675411	NA	3.34E-10	mr1733	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
vg0315675411	NA	4.46E-08	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
vg0315675411	NA	1.60E-06	mr1138_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
vg0315675411	NA	1.03E-08	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
vg0315675411	NA	1.82E-14	mr1410_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
vg0315675411	NA	5.60E-07	mr1422_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
vg0315675411	NA	8.10E-06	mr1873_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
vg0315675411	NA	6.37E-10	mr1993_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
vg0315675411	NA	2.47E-12	mr1993_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