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Detailed information for vg0135555900:

Variant ID: vg0135555900 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 35555900
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTATGGAAGTGATAATTCAGTGTGTTCAACTCTTTCGCGTTTATTATATTAAAAAATAGTTTTTTTTAAAAAAAATATGTGTTTCAAATCCCGCTAAC[T/C]
CTATTTGAATTAATTTCTCTCAACGTATATATGTGTGGTTACCTATTATCCTAGTGATCACAGAGCCAGAAATTCTAAAATTTATAAGTAGGGAGGTGTT

Reverse complement sequence

AACACCTCCCTACTTATAAATTTTAGAATTTCTGGCTCTGTGATCACTAGGATAATAGGTAACCACACATATATACGTTGAGAGAAATTAATTCAAATAG[A/G]
GTTAGCGGGATTTGAAACACATATTTTTTTTAAAAAAAACTATTTTTTAATATAATAAACGCGAAAGAGTTGAACACACTGAATTATCACTTCCATAATT

Allele Frequencies:

QTN in RiceNavi

Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.

Category	Variant ID	Chrom	Pos	Gene	MSU	RAP	Alt_Allele_Function	Ref_geno	Alt_geno
Yield components	vg0135555900	Chr1	35555900	LAX1	LOC_Os01g61480	Os01g0831000	increasing grain number	T	C

Allele Effect:

Putative Genotype-Phenotype Associations: