Hello, I have a plant data of 300 varieties, on which I already performed GWAS. After GWAS, I have annotated the most significant snps to find candidate genes. I found some candidate genes that are predicted to be associated with my trait.
Now, I want to find the haplotypes of those candidate genes in my entire plant population. For this, I want to find all the snps in my candidate genes, and its location in my gene with respect to exon, intron, promoter, 5'UTR etc. Also I want to know, individuals(accessions) carrying those haplotypes? Can anyone suggest me, how to accomplish my task? Any tools, or programs that can do it?
I already used haploview for it, but it can only give haplotype blocks and frequency. It cannot give the full information of individuals carrying a specific haplotype. I tried it in BLAST also, by selecting pairwise with dots for identities. For this, I blasted my gene in NCBI, and selected Pairwise with dots for identities. It gives the mismatched bases in red color, and identical bases are shown as dots, as given below. But I am not sure, these are snps, or sequencing errors. Can we use blast for finding snps? Highly appreciated, if get some precious suggestions.
Alignment statistics for match #1
Score Expect Identities Gaps Strand
3055 bits(1654) 0.0 1747/1792(97%) 6/1792(0%) Plus/Plus
Query 1 ATGGAGAAAAAGCAAGGTTTTTTCTCAGCTCTCAAAGAGGAAGTAATTCGTGGGCTTTCA 60
Sbjct 4420511 ............................................................ 4420570
Query 61 CCTTCCCGCTCGAGGACCAACAGCCCCGGAAGAGCCCGGTCACCTATTGCCATTCTGTTG 120
Sbjct 4420571 ............................................C............... 4420630
Query 121 CGGAGAAAGAAAAGCGGCCACTACAACTACGGAGGCGCTTACCTGGTACAACCGGAGCCC 180
Sbjct 4420631 .....................A........................CG............ 4420690
Query 181 TTGATCGCGAGGTACGGTGTCGGGGAAGCGTTAGCTCCGCTCATGGAAGGTCCCGACCCG 240
Sbjct 4420691 ....C........................T.............................. 4420750
Query 241 GACGGAGGCGAAACCGGGGATTCCAAGAGGCTTGGGTTGGGGCTAGGACAATGGGTTATG 300
Sbjct 4420751 ........T...........C................C...................... 4420810
Query 301 GGACAGTTATCGAGGACTCCATCCATGGCTTCCTTGAGTTGCAAAAGGTCCGATCTAAGG 360
Sbjct 4420811 ............................................................
